Action: PROJECT_POINTS

Module	dimred
Description	Usage
Find the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input

Details and examples

Find the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input

This action and ARRANGE_POINTS are the workhorses for the implementation of SKETCHMAP that is provided within PLUMED. PROJECT_POINTS allows you to provide the low dimensional coordinate $y_\textrm{min}$ at which the following stress function is minimised:

$$\chi(y) = \sum_{i=1}^N w_i [ D(X_i, Y) - d(x_i,y) ]^2$$

where $Y$ is a set of coordinates in some high dimensional space, $X_i$ is a set of coordinates for one of $N$ landmark points in this high-dimensional space, $x_i$ is a projection for $X_i$ that we have found in some lower dimensional space and $w_i$ is a weight. The $D$ indicates that we are calculating the dissimilarity between the point $X_i$ and $Y$, while $d$ represents the distance between the point $x_i$ and $y$. In minimising the expression above we are thus finding the point $y$ at which the distances between $y$ and each of the projections, $x_i$, of the $N$ landmark points most closely resembles the dissimiarities between $Y$ and the $N$ landmark points in the high-dimensional points.

The example input below illustrates how you can use PROJECT_POINTS to find the projection of a high-dimensional point in practice.

Click on the labels of the actions for more information on what each action computes

# The coordinates of the landmarks in the high dimensional space
d1_refThe CONSTANT action with label d1_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
d1_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1.0,2.0,1.5,2.1
d1_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1.0,2.0,1.5,2.1  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
d2_refThe CONSTANT action with label d2_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
d2_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.5,0.7,0.2,1.3
d2_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.5,0.7,0.2,1.3  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
d3_refThe CONSTANT action with label d3_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
d3_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=3.1,2.0,1.5,0.5
d3_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=3.1,2.0,1.5,0.5  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0

# The weights of the landmark
weightsThe CONSTANT action with label weights calculates the following quantities:
 Quantity   
 Type   
 Description  
weights
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1,1,1,1
weights: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1,1,1,1  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0

# The projections of the landmarks in the low dimensional space
proj1_refThe CONSTANT action with label proj1_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
proj1_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.5,0.8,0.2,0.4
proj1_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.5,0.8,0.2,0.4  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
proj2_refThe CONSTANT action with label proj2_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
proj2_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.2,0.9,0.3,0.7
proj2_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.2,0.9,0.3,0.7  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0

# Calcuate the instantaneous values of the three distances
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,4
d3The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,6

# Calculate the distances between the instananeous points and the current positions
edThe EUCLIDEAN_DISTANCE action with label ed calculates the following quantities:
 Quantity   
 Type   
 Description  
ed
vector
the euclidean distances between the input vectors: EUCLIDEAN_DISTANCECalculate the euclidean distance between two vectors of arguments This action is a shortcut. More details SQUARED The squared distance should be calculated ARG2The point that we are calculating the distance to=d1,d2,d3 ARG1The poin that we are calculating the distance from=d1_ref,d2_ref,d3_ref
# PLUMED interprets the command:
# ed: EUCLIDEAN_DISTANCE SQUARED ARG2=d1,d2,d3 ARG1=d1_ref,d2_ref,d3_ref
# as follows (Click the red comment above to revert to the short version of the input):
ed_diffThe VSTACK action with label ed_diff calculates the following quantities:
 Quantity   
 Type   
 Description  
ed_diff
matrix
a matrix that contains the input vectors in its columns: DISPLACEMENTCalculate the displacement vector between the pair of input vectors More details ARG1The point that we are calculating the distance from=d1_ref,d2_ref,d3_ref ARG2The point that we are calculating the distance to=d1,d2,d3
ed_diffTThe TRANSPOSE action with label ed_diffT calculates the following quantities:
 Quantity   
 Type   
 Description  
ed_diffT
matrix
the transpose of the input matrix: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=ed_diff
edThe MATRIX_PRODUCT_DIAGONAL action with label ed calculates the following quantities:
 Quantity   
 Type   
 Description  
ed
vector
a vector containing the diagonal elements of the matrix that obtaned by multiplying the two input matrices together: MATRIX_PRODUCT_DIAGONALCalculate the product of two matrices and return a vector that contains the diagonal elements of the ouptut vector More details ARGthe two vectors/matrices whose product are to be taken=ed_diff,ed_diffT
# --- End of included input --- 
# And generate the projection
projThe PROJECT_POINTS action with label proj calculates the following quantities:
 Quantity   
 Type   
 Description  
proj.coord-1
scalar
the coordinates of the points in the low dimensional space  This is the 1th of these quantities
proj.coord-2
scalar
the coordinates of the points in the low dimensional space  This is the 2th of these quantities: PROJECT_POINTSFind the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input This action has hidden defaults. More details ARGthe projections of the landmark points=proj1_ref,proj2_ref TARGET1the matrix of target quantities that you would like to match=ed WEIGHTS1the matrix with the weights of the target quantities=weights
proj: PROJECT_POINTSFind the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input This action uses the defaults shown here. More details ARGthe projections of the landmark points=proj1_ref,proj2_ref TARGET1the matrix of target quantities that you would like to match=ed WEIGHTS1the matrix with the weights of the target quantities=weights  CGTOL the tolerance for the conjugate gradient minimization=1E-6

# And output the projection to a file
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=proj.* FILEthe name of the file on which to output these quantities=colvar

In this example, we use three distances to define the high dimensional coordinates and have four landmarks points.

Projecting multiple coordinates at once

The input to the EUCLIDEAN_DISTANCE shortcut in the example in the previous section consisted of three scalar-valued quantities. The two components output by project points are thus also scalars. By contrast, in the input below four three-dimenional vectors are input to the EUCLIDEAN_DISTANCE shortcut. The components output by proj and thus four-dimensional vectors.

Click on the labels of the actions for more information on what each action computes

# The coordinates of the landmarks in the high dimensional space
d1_refThe CONSTANT action with label d1_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
d1_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1.0,2.0,1.5,2.1
d1_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1.0,2.0,1.5,2.1  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
d2_refThe CONSTANT action with label d2_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
d2_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.5,0.7,0.2,1.3
d2_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.5,0.7,0.2,1.3  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
d3_refThe CONSTANT action with label d3_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
d3_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=3.1,2.0,1.5,0.5
d3_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=3.1,2.0,1.5,0.5  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0

# The weights of the landmark
weightsThe CONSTANT action with label weights calculates the following quantities:
 Quantity   
 Type   
 Description  
weights
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1,1,1,1
weights: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1,1,1,1  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0

# The projections of the landmarks in the low dimensional space
proj1_refThe CONSTANT action with label proj1_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
proj1_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.5,0.8,0.2,0.4
proj1_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.5,0.8,0.2,0.4  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
proj2_refThe CONSTANT action with label proj2_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
proj2_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.2,0.9,0.3,0.7
proj2_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.2,0.9,0.3,0.7  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0

# Calcuate the instantaneous values of the distances
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1,2 ATOMS2the pair of atom that we are calculating the distance between=7,8   ATOMS3the pair of atom that we are calculating the distance between=13,14 ATOMS4the pair of atom that we are calculating the distance between=19,20
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=3,4 ATOMS2the pair of atom that we are calculating the distance between=9,10  ATOMS3the pair of atom that we are calculating the distance between=15,16 ATOMS4the pair of atom that we are calculating the distance between=21,22
d3The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=5,6 ATOMS2the pair of atom that we are calculating the distance between=11,12 ATOMS3the pair of atom that we are calculating the distance between=17,18 ATOMS4the pair of atom that we are calculating the distance between=23,24

# Calculate the distances between the instananeous points and the current positions
edThe EUCLIDEAN_DISTANCE action with label ed calculates the following quantities:
 Quantity   
 Type   
 Description  
ed
vector
the euclidean distances between the input vectors: EUCLIDEAN_DISTANCECalculate the euclidean distance between two vectors of arguments This action is a shortcut. More details SQUARED The squared distance should be calculated ARG1The poin that we are calculating the distance from=d1,d2,d3 ARG2The point that we are calculating the distance to=d1_ref,d2_ref,d3_ref
# PLUMED interprets the command:
# ed: EUCLIDEAN_DISTANCE SQUARED ARG1=d1,d2,d3 ARG2=d1_ref,d2_ref,d3_ref
# as follows (Click the red comment above to revert to the short version of the input):
ed_diffThe VSTACK action with label ed_diff calculates the following quantities:
 Quantity   
 Type   
 Description  
ed_diff
matrix
a matrix that contains the input vectors in its columns: DISPLACEMENTCalculate the displacement vector between the pair of input vectors More details ARG1The point that we are calculating the distance from=d1,d2,d3 ARG2The point that we are calculating the distance to=d1_ref,d2_ref,d3_ref
ed_diffTThe TRANSPOSE action with label ed_diffT calculates the following quantities:
 Quantity   
 Type   
 Description  
ed_diffT
matrix
the transpose of the input matrix: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=ed_diff
edThe MATRIX_PRODUCT_DIAGONAL action with label ed calculates the following quantities:
 Quantity   
 Type   
 Description  
ed
vector
a vector containing the diagonal elements of the matrix that obtaned by multiplying the two input matrices together: MATRIX_PRODUCT_DIAGONALCalculate the product of two matrices and return a vector that contains the diagonal elements of the ouptut vector More details ARGthe two vectors/matrices whose product are to be taken=ed_diff,ed_diffT
# --- End of included input --- 
# And generate the projection
projThe PROJECT_POINTS action with label proj calculates the following quantities:
 Quantity   
 Type   
 Description  
proj.coord-1
scalar
the coordinates of the points in the low dimensional space  This is the 1th of these quantities
proj.coord-2
scalar
the coordinates of the points in the low dimensional space  This is the 2th of these quantities: PROJECT_POINTSFind the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input This action has hidden defaults. More details ARGthe projections of the landmark points=proj1_ref,proj2_ref TARGET1the matrix of target quantities that you would like to match=ed WEIGHTS1the matrix with the weights of the target quantities=weights
proj: PROJECT_POINTSFind the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input This action uses the defaults shown here. More details ARGthe projections of the landmark points=proj1_ref,proj2_ref TARGET1the matrix of target quantities that you would like to match=ed WEIGHTS1the matrix with the weights of the target quantities=weights  CGTOL the tolerance for the conjugate gradient minimization=1E-6

# And output the projection to a file
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=proj.* FILEthe name of the file on which to output these quantities=colvar

Using RMSD distances

One can use RMSD distances as the dissimilarities rather than distances in some space of arguments as is illustrated below:

Click on the labels of the actions for more information on what each action computes

#SETTINGS INPUTFILES=regtest/trajectories/path_msd/allv.pdb

# This action reads in the landmarks in the high dimensional space and calculates the
# distances from the instantaneous configuration
rmsdThe RMSD action with label rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd
vector
the RMSD distance between the instaneous structure and the reference structure/s that were input: RMSDCalculate the RMSD with respect to a reference structure. This action is a shortcut and it has hidden defaults. More details SQUARED  This should be setted if you want MSD instead of RMSD  TYPE the manner in which RMSD alignment is performed=OPTIMAL REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=
regtest/trajectories/path_msd/allv.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/trajectories/path_msd/allv.pdb
    
REMARK X=1 Y=2 
ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00
ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00
ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00
ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00
ATOM      8  HL  ALA     1      -1.845   0.961  -0.011  1.00  1.00
ATOM      9  CA  ALA     1      -0.003  -0.019   0.021  1.00  1.00
ATOM     10  HA  ALA     1       0.205  -1.051   0.259  1.00  1.00
ATOM     11  CB  ALA     1       0.009   0.135  -1.509  1.00  1.00
ATOM     15  CRP ALA     1       1.121   0.799   0.663  1.00  1.00
ATOM     16  OR  ALA     1       1.723   1.669   0.043  1.00  1.00
ATOM     17  NR  ALA     1       1.423   0.519   1.941  1.00  1.00
ATOM     18  HR  ALA     1       0.873  -0.161   2.413  1.00  1.00
ATOM     19  CR  ALA     1       2.477   1.187   2.675  1.00  1.00
END
FIXED
REMARK X=2 Y=3 
ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00
ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00
ATOM      6  OL  ALA     1      -1.201  -0.849   2.425  1.00  1.00
ATOM      7  NL  ALA     1      -1.296   0.337   0.534  1.00  1.00
ATOM      8  HL  ALA     1      -1.807   0.951  -0.044  1.00  1.00
ATOM      9  CA  ALA     1       0.009  -0.067   0.033  1.00  1.00
ATOM     10  HA  ALA     1       0.175  -1.105   0.283  1.00  1.00
ATOM     11  CB  ALA     1       0.027   0.046  -1.501  1.00  1.00
ATOM     15  CRP ALA     1       1.149   0.725   0.654  1.00  1.00
ATOM     16  OR  ALA     1       1.835   1.491  -0.011  1.00  1.00
ATOM     17  NR  ALA     1       1.380   0.537   1.968  1.00  1.00
ATOM     18  HR  ALA     1       0.764  -0.060   2.461  1.00  1.00
ATOM     19  CR  ALA     1       2.431   1.195   2.683  1.00  1.00
END
REMARK X=3 Y=4 
ATOM      1  CL  ALA     1      -2.990   0.383   2.277  1.00  1.00
ATOM      5  CLP ALA     1      -1.664  -0.085   1.831  1.00  1.00
ATOM      6  OL  ALA     1      -0.987  -0.835   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.227   0.364   0.646  1.00  1.00
ATOM      8  HL  ALA     1      -1.798   0.982   0.124  1.00  1.00
ATOM      9  CA  ALA     1       0.026  -0.028   0.044  1.00  1.00
ATOM     10  HA  ALA     1       0.224  -1.060   0.284  1.00  1.00
ATOM     11  CB  ALA     1      -0.076   0.107  -1.483  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.776   0.577  1.00  1.00
ATOM     16  OR  ALA     1       1.900   1.463  -0.158  1.00  1.00
ATOM     17  NR  ALA     1       1.494   0.666   1.888  1.00  1.00
ATOM     18  HR  ALA     1       0.882   0.122   2.437  1.00  1.00
ATOM     19  CR  ALA     1       2.580   1.341   2.529  1.00  1.00
END
REMARK X=4 Y=5 
ATOM      1  CL  ALA     1      -3.006   0.350   2.252  1.00  1.00
ATOM      5  CLP ALA     1      -1.680  -0.112   1.826  1.00  1.00
ATOM      6  OL  ALA     1      -1.025  -0.896   2.508  1.00  1.00
ATOM      7  NL  ALA     1      -1.220   0.368   0.654  1.00  1.00
ATOM      8  HL  ALA     1      -1.771   1.013   0.137  1.00  1.00
ATOM      9  CA  ALA     1       0.040  -0.029   0.062  1.00  1.00
ATOM     10  HA  ALA     1       0.210  -1.076   0.277  1.00  1.00
ATOM     11  CB  ALA     1      -0.066   0.148  -1.465  1.00  1.00
ATOM     15  CRP ALA     1       1.241   0.738   0.605  1.00  1.00
ATOM     16  OR  ALA     1       1.986   1.347  -0.125  1.00  1.00
ATOM     17  NR  ALA     1       1.446   0.694   1.940  1.00  1.00
ATOM     18  HR  ALA     1       0.796   0.210   2.481  1.00  1.00
ATOM     19  CR  ALA     1       2.544   1.350   2.582  1.00  1.00
END
REMARK X=5 Y=6 
ATOM      1  CL  ALA     1      -3.002   0.343   2.271  1.00  1.00
ATOM      5  CLP ALA     1      -1.672  -0.125   1.828  1.00  1.00
ATOM      6  OL  ALA     1      -1.028  -0.942   2.486  1.00  1.00
ATOM      7  NL  ALA     1      -1.213   0.373   0.670  1.00  1.00
ATOM      8  HL  ALA     1      -1.752   1.033   0.169  1.00  1.00
ATOM      9  CA  ALA     1       0.041  -0.032   0.055  1.00  1.00
ATOM     10  HA  ALA     1       0.201  -1.079   0.245  1.00  1.00
ATOM     11  CB  ALA     1      -0.079   0.194  -1.466  1.00  1.00
ATOM     15  CRP ALA     1       1.257   0.720   0.601  1.00  1.00
ATOM     16  OR  ALA     1       2.057   1.240  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.422   0.730   1.942  1.00  1.00
ATOM     18  HR  ALA     1       0.740   0.303   2.500  1.00  1.00
ATOM     19  CR  ALA     1       2.528   1.373   2.598  1.00  1.00
END
REMARK X=6 Y=7 
ATOM      1  CL  ALA     1      -3.144   1.457   1.417  1.00  1.00
ATOM      5  CLP ALA     1      -1.943   0.587   1.450  1.00  1.00
ATOM      6  OL  ALA     1      -1.588   0.028   2.480  1.00  1.00
ATOM      7  NL  ALA     1      -1.281   0.449   0.306  1.00  1.00
ATOM      8  HL  ALA     1      -1.578   0.914  -0.520  1.00  1.00
ATOM      9  CA  ALA     1      -0.132  -0.428   0.139  1.00  1.00
ATOM     10  HA  ALA     1      -0.264  -1.291   0.758  1.00  1.00
ATOM     11  CB  ALA     1      -0.066  -0.855  -1.329  1.00  1.00
ATOM     15  CRP ALA     1       1.193   0.220   0.554  1.00  1.00
ATOM     16  OR  ALA     1       2.195   0.098  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.224   0.872   1.737  1.00  1.00
ATOM     18  HR  ALA     1       0.399   0.943   2.273  1.00  1.00
ATOM     19  CR  ALA     1       2.413   1.511   2.254  1.00  1.00
END
REMARK X=7 Y=8 
ATOM      1  CL  ALA     1      -3.140   1.441   1.453  1.00  1.00
ATOM      5  CLP ALA     1      -1.944   0.576   1.465  1.00  1.00
ATOM      6  OL  ALA     1      -1.587  -0.018   2.487  1.00  1.00
ATOM      7  NL  ALA     1      -1.274   0.465   0.322  1.00  1.00
ATOM      8  HL  ALA     1      -1.571   0.957  -0.486  1.00  1.00
ATOM      9  CA  ALA     1      -0.124  -0.418   0.135  1.00  1.00
ATOM     10  HA  ALA     1      -0.274  -1.304   0.729  1.00  1.00
ATOM     11  CB  ALA     1      -0.063  -0.813  -1.347  1.00  1.00
ATOM     15  CRP ALA     1       1.201   0.199   0.572  1.00  1.00
ATOM     16  OR  ALA     1       2.227   0.007  -0.072  1.00  1.00
ATOM     17  NR  ALA     1       1.215   0.910   1.709  1.00  1.00
ATOM     18  HR  ALA     1       0.369   1.020   2.200  1.00  1.00
ATOM     19  CR  ALA     1       2.393   1.536   2.237  1.00  1.00
END
REMARK X=8 Y=9 
ATOM      1  CL  ALA     1      -3.140   1.420   1.442  1.00  1.00
ATOM      5  CLP ALA     1      -1.948   0.546   1.448  1.00  1.00
ATOM      6  OL  ALA     1      -1.618  -0.065   2.460  1.00  1.00
ATOM      7  NL  ALA     1      -1.255   0.469   0.311  1.00  1.00
ATOM      8  HL  ALA     1      -1.538   0.979  -0.490  1.00  1.00
ATOM      9  CA  ALA     1      -0.107  -0.412   0.124  1.00  1.00
ATOM     10  HA  ALA     1      -0.257  -1.312   0.685  1.00  1.00
ATOM     11  CB  ALA     1      -0.028  -0.770  -1.375  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.186   0.600  1.00  1.00
ATOM     16  OR  ALA     1       2.269  -0.069   0.026  1.00  1.00
ATOM     17  NR  ALA     1       1.193   0.966   1.687  1.00  1.00
ATOM     18  HR  ALA     1       0.333   1.114   2.120  1.00  1.00
ATOM     19  CR  ALA     1       2.377   1.589   2.240  1.00  1.00
END
REMARK X=9 Y=10 
ATOM      1  CL  ALA     1      -3.110   1.698   0.880  1.00  1.00
ATOM      5  CLP ALA     1      -2.021   0.734   1.142  1.00  1.00
ATOM      6  OL  ALA     1      -1.859   0.257   2.258  1.00  1.00
ATOM      7  NL  ALA     1      -1.229   0.414   0.114  1.00  1.00
ATOM      8  HL  ALA     1      -1.371   0.826  -0.771  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.593   0.188  1.00  1.00
ATOM     10  HA  ALA     1      -0.481  -1.374   0.851  1.00  1.00
ATOM     11  CB  ALA     1       0.011  -1.180  -1.220  1.00  1.00
ATOM     15  CRP ALA     1       1.163  -0.060   0.716  1.00  1.00
ATOM     16  OR  ALA     1       2.227  -0.564   0.393  1.00  1.00
ATOM     17  NR  ALA     1       1.127   0.960   1.594  1.00  1.00
ATOM     18  HR  ALA     1       0.234   1.295   1.847  1.00  1.00
ATOM     19  CR  ALA     1       2.303   1.549   2.172  1.00  1.00
END
REMARK X=10 Y=11 
ATOM      1  CL  ALA     1      -3.139   1.652   0.924  1.00  1.00
ATOM      5  CLP ALA     1      -2.039   0.698   1.169  1.00  1.00
ATOM      6  OL  ALA     1      -1.868   0.201   2.278  1.00  1.00
ATOM      7  NL  ALA     1      -1.239   0.411   0.139  1.00  1.00
ATOM      8  HL  ALA     1      -1.385   0.842  -0.737  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.574   0.193  1.00  1.00
ATOM     10  HA  ALA     1      -0.477  -1.381   0.833  1.00  1.00
ATOM     11  CB  ALA     1       0.029  -1.142  -1.231  1.00  1.00
ATOM     15  CRP ALA     1       1.162  -0.048   0.731  1.00  1.00
ATOM     16  OR  ALA     1       2.220  -0.597   0.472  1.00  1.00
ATOM     17  NR  ALA     1       1.122   1.024   1.537  1.00  1.00
ATOM     18  HR  ALA     1       0.233   1.395   1.752  1.00  1.00
ATOM     19  CR  ALA     1       2.300   1.629   2.102  1.00  1.00
END
REMARK X=11 Y=12 
ATOM      1  CL  ALA     1      -3.706   1.088   0.468  1.00  1.00
ATOM      5  CLP ALA     1      -2.458   0.598   1.082  1.00  1.00
ATOM      6  OL  ALA     1      -2.390   0.404   2.277  1.00  1.00
ATOM      7  NL  ALA     1      -1.427   0.382   0.258  1.00  1.00
ATOM      8  HL  ALA     1      -1.513   0.559  -0.713  1.00  1.00
ATOM      9  CA  ALA     1      -0.157  -0.192   0.685  1.00  1.00
ATOM     10  HA  ALA     1      -0.343  -0.912   1.470  1.00  1.00
ATOM     11  CB  ALA     1       0.462  -0.936  -0.512  1.00  1.00
ATOM     15  CRP ALA     1       0.840   0.814   1.241  1.00  1.00
ATOM     16  OR  ALA     1       2.034   0.549   1.354  1.00  1.00
ATOM     17  NR  ALA     1       0.368   2.017   1.650  1.00  1.00
ATOM     18  HR  ALA     1      -0.613   2.169   1.589  1.00  1.00
ATOM     19  CR  ALA     1       1.215   3.044   2.195  1.00  1.00
END
REMARK X=12 Y=13 
ATOM      1  CL  ALA     1      -3.699   1.173   0.487  1.00  1.00
ATOM      5  CLP ALA     1      -2.464   0.631   1.079  1.00  1.00
ATOM      6  OL  ALA     1      -2.402   0.386   2.275  1.00  1.00
ATOM      7  NL  ALA     1      -1.434   0.437   0.260  1.00  1.00
ATOM      8  HL  ALA     1      -1.516   0.652  -0.701  1.00  1.00
ATOM      9  CA  ALA     1      -0.174  -0.174   0.667  1.00  1.00
ATOM     10  HA  ALA     1      -0.377  -0.924   1.411  1.00  1.00
ATOM     11  CB  ALA     1       0.451  -0.859  -0.570  1.00  1.00
ATOM     15  CRP ALA     1       0.839   0.801   1.280  1.00  1.00
ATOM     16  OR  ALA     1       1.999   0.474   1.468  1.00  1.00
ATOM     17  NR  ALA     1       0.404   2.024   1.627  1.00  1.00
ATOM     18  HR  ALA     1      -0.565   2.225   1.505  1.00  1.00
ATOM     19  CR  ALA     1       1.262   3.025   2.214  1.00  1.00
END
REMARK X=13 Y=14 
ATOM      1  CL  ALA     1      -3.653   0.990   1.121  1.00  1.00
ATOM      5  CLP ALA     1      -2.321   0.364   1.249  1.00  1.00
ATOM      6  OL  ALA     1      -2.006  -0.222   2.265  1.00  1.00
ATOM      7  NL  ALA     1      -1.498   0.501   0.205  1.00  1.00
ATOM      8  HL  ALA     1      -1.794   0.978  -0.603  1.00  1.00
ATOM      9  CA  ALA     1      -0.190  -0.127   0.128  1.00  1.00
ATOM     10  HA  ALA     1      -0.216  -1.086   0.627  1.00  1.00
ATOM     11  CB  ALA     1       0.159  -0.359  -1.359  1.00  1.00
ATOM     15  CRP ALA     1       0.933   0.668   0.793  1.00  1.00
ATOM     16  OR  ALA     1       2.107   0.313   0.705  1.00  1.00
ATOM     17  NR  ALA     1       0.604   1.770   1.498  1.00  1.00
ATOM     18  HR  ALA     1      -0.359   1.986   1.593  1.00  1.00
ATOM     19  CR  ALA     1       1.573   2.595   2.158  1.00  1.00
END
REMARK X=14 Y=15 
ATOM      1  CL  ALA     1      -3.641   0.954   1.179  1.00  1.00
ATOM      5  CLP ALA     1      -2.294   0.335   1.290  1.00  1.00
ATOM      6  OL  ALA     1      -1.964  -0.273   2.288  1.00  1.00
ATOM      7  NL  ALA     1      -1.485   0.499   0.235  1.00  1.00
ATOM      8  HL  ALA     1      -1.803   0.995  -0.564  1.00  1.00
ATOM      9  CA  ALA     1      -0.175  -0.118   0.130  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.077   0.601  1.00  1.00
ATOM     11  CB  ALA     1       0.162  -0.300  -1.355  1.00  1.00
ATOM     15  CRP ALA     1       0.952   0.671   0.815  1.00  1.00
ATOM     16  OR  ALA     1       2.104   0.260   0.791  1.00  1.00
ATOM     17  NR  ALA     1       0.633   1.808   1.450  1.00  1.00
ATOM     18  HR  ALA     1      -0.328   2.065   1.503  1.00  1.00
ATOM     19  CR  ALA     1       1.608   2.627   2.129  1.00  1.00
END
REMARK X=15 Y=16 
ATOM      1  CL  ALA     1      -3.635   0.925   1.244  1.00  1.00
ATOM      5  CLP ALA     1      -2.297   0.305   1.309  1.00  1.00
ATOM      6  OL  ALA     1      -1.941  -0.334   2.290  1.00  1.00
ATOM      7  NL  ALA     1      -1.500   0.490   0.251  1.00  1.00
ATOM      8  HL  ALA     1      -1.827   1.009  -0.537  1.00  1.00
ATOM      9  CA  ALA     1      -0.178  -0.110   0.119  1.00  1.00
ATOM     10  HA  ALA     1      -0.205  -1.094   0.536  1.00  1.00
ATOM     11  CB  ALA     1       0.147  -0.217  -1.379  1.00  1.00
ATOM     15  CRP ALA     1       0.943   0.643   0.832  1.00  1.00
ATOM     16  OR  ALA     1       2.074   0.198   0.871  1.00  1.00
ATOM     17  NR  ALA     1       0.637   1.821   1.423  1.00  1.00
ATOM     18  HR  ALA     1      -0.311   2.123   1.418  1.00  1.00
ATOM     19  CR  ALA     1       1.602   2.629   2.109  1.00  1.00
END
REMARK X=16 Y=17 
ATOM      1  CL  ALA     1      -3.632   0.856   1.331  1.00  1.00
ATOM      5  CLP ALA     1      -2.282   0.250   1.355  1.00  1.00
ATOM      6  OL  ALA     1      -1.906  -0.403   2.301  1.00  1.00
ATOM      7  NL  ALA     1      -1.515   0.478   0.275  1.00  1.00
ATOM      8  HL  ALA     1      -1.860   0.990  -0.485  1.00  1.00
ATOM      9  CA  ALA     1      -0.192  -0.105   0.098  1.00  1.00
ATOM     10  HA  ALA     1      -0.204  -1.121   0.473  1.00  1.00
ATOM     11  CB  ALA     1       0.129  -0.136  -1.408  1.00  1.00
ATOM     15  CRP ALA     1       0.931   0.615   0.844  1.00  1.00
ATOM     16  OR  ALA     1       2.043   0.122   0.934  1.00  1.00
ATOM     17  NR  ALA     1       0.651   1.819   1.388  1.00  1.00
ATOM     18  HR  ALA     1      -0.283   2.155   1.349  1.00  1.00
ATOM     19  CR  ALA     1       1.624   2.595   2.115  1.00  1.00
END
REMARK X=17 Y=18 
ATOM      1  CL  ALA     1      -3.628   0.823   1.358  1.00  1.00
ATOM      5  CLP ALA     1      -2.277   0.241   1.370  1.00  1.00
ATOM      6  OL  ALA     1      -1.871  -0.396   2.325  1.00  1.00
ATOM      7  NL  ALA     1      -1.525   0.469   0.284  1.00  1.00
ATOM      8  HL  ALA     1      -1.898   0.970  -0.482  1.00  1.00
ATOM      9  CA  ALA     1      -0.195  -0.094   0.086  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.122   0.423  1.00  1.00
ATOM     11  CB  ALA     1       0.146  -0.058  -1.413  1.00  1.00
ATOM     15  CRP ALA     1       0.919   0.599   0.874  1.00  1.00
ATOM     16  OR  ALA     1       1.997   0.065   1.039  1.00  1.00
ATOM     17  NR  ALA     1       0.655   1.830   1.373  1.00  1.00
ATOM     18  HR  ALA     1      -0.248   2.200   1.261  1.00  1.00
ATOM     19  CR  ALA     1       1.625   2.581   2.124  1.00  1.00
END
REMARK X=18 Y=19 
ATOM      1  CL  ALA     1      -3.539   0.055   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -2.117  -0.208   1.378  1.00  1.00
ATOM      6  OL  ALA     1      -1.453  -0.902   2.125  1.00  1.00
ATOM      7  NL  ALA     1      -1.602   0.351   0.289  1.00  1.00
ATOM      8  HL  ALA     1      -2.185   0.875  -0.310  1.00  1.00
ATOM      9  CA  ALA     1      -0.243   0.129  -0.186  1.00  1.00
ATOM     10  HA  ALA     1      -0.041  -0.924  -0.159  1.00  1.00
ATOM     11  CB  ALA     1      -0.153   0.625  -1.651  1.00  1.00
ATOM     15  CRP ALA     1       0.852   0.806   0.637  1.00  1.00
ATOM     16  OR  ALA     1       2.007   0.400   0.594  1.00  1.00
ATOM     17  NR  ALA     1       0.508   1.855   1.401  1.00  1.00
ATOM     18  HR  ALA     1      -0.445   2.112   1.454  1.00  1.00
ATOM     19  CR  ALA     1       1.460   2.569   2.226  1.00  1.00
END
REMARK X=19 Y=20 
ATOM      1  CL  ALA     1      -3.578   0.084   1.603  1.00  1.00
ATOM      5  CLP ALA     1      -2.140  -0.156   1.375  1.00  1.00
ATOM      6  OL  ALA     1      -1.473  -0.732   2.197  1.00  1.00
ATOM      7  NL  ALA     1      -1.623   0.335   0.237  1.00  1.00
ATOM      8  HL  ALA     1      -2.220   0.753  -0.416  1.00  1.00
ATOM      9  CA  ALA     1      -0.253   0.120  -0.195  1.00  1.00
ATOM     10  HA  ALA     1      -0.048  -0.931  -0.153  1.00  1.00
ATOM     11  CB  ALA     1      -0.128   0.612  -1.663  1.00  1.00
ATOM     15  CRP ALA     1       0.823   0.801   0.637  1.00  1.00
ATOM     16  OR  ALA     1       1.969   0.367   0.665  1.00  1.00
ATOM     17  NR  ALA     1       0.477   1.912   1.333  1.00  1.00
ATOM     18  HR  ALA     1      -0.468   2.199   1.317  1.00  1.00
ATOM     19  CR  ALA     1       1.410   2.627   2.163  1.00  1.00
END
REMARK X=20 Y=21 
ATOM      1  CL  ALA     1      -3.113   1.661   1.504  1.00  1.00
ATOM      5  CLP ALA     1      -1.769   1.059   1.566  1.00  1.00
ATOM      6  OL  ALA     1      -1.201   0.940   2.629  1.00  1.00
ATOM      7  NL  ALA     1      -1.219   0.714   0.392  1.00  1.00
ATOM      8  HL  ALA     1      -1.742   0.797  -0.435  1.00  1.00
ATOM      9  CA  ALA     1       0.058   0.023   0.242  1.00  1.00
ATOM     10  HA  ALA     1      -0.001  -0.896   0.782  1.00  1.00
ATOM     11  CB  ALA     1       0.235  -0.295  -1.249  1.00  1.00
ATOM     15  CRP ALA     1       1.299   0.757   0.745  1.00  1.00
ATOM     16  OR  ALA     1       2.276   0.138   1.135  1.00  1.00
ATOM     17  NR  ALA     1       1.277   2.102   0.736  1.00  1.00
ATOM     18  HR  ALA     1       0.447   2.567   0.458  1.00  1.00
ATOM     19  CR  ALA     1       2.391   2.896   1.191  1.00  1.00
END
REMARK X=21 Y=22 
ATOM      1  CL  ALA     1      -3.089   1.850   1.546  1.00  1.00
ATOM      5  CLP ALA     1      -1.667   1.457   1.629  1.00  1.00
ATOM      6  OL  ALA     1      -0.974   1.868   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.204   0.683   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -1.844   0.360  -0.021  1.00  1.00
ATOM      9  CA  ALA     1       0.126   0.105   0.564  1.00  1.00
ATOM     10  HA  ALA     1       0.239  -0.555   1.391  1.00  1.00
ATOM     11  CB  ALA     1       0.215  -0.722  -0.739  1.00  1.00
ATOM     15  CRP ALA     1       1.311   1.068   0.623  1.00  1.00
ATOM     16  OR  ALA     1       2.369   0.726   1.149  1.00  1.00
ATOM     17  NR  ALA     1       1.156   2.292   0.077  1.00  1.00
ATOM     18  HR  ALA     1       0.273   2.549  -0.285  1.00  1.00
ATOM     19  CR  ALA     1       2.201   3.277   0.107  1.00  1.00
END
REMARK X=22 Y=23 
ATOM      1  CL  ALA     1      -3.102   1.775   1.619  1.00  1.00
ATOM      5  CLP ALA     1      -1.661   1.466   1.659  1.00  1.00
ATOM      6  OL  ALA     1      -0.945   1.961   2.476  1.00  1.00
ATOM      7  NL  ALA     1      -1.205   0.663   0.688  1.00  1.00
ATOM      8  HL  ALA     1      -1.854   0.269   0.091  1.00  1.00
ATOM      9  CA  ALA     1       0.147   0.134   0.561  1.00  1.00
ATOM     10  HA  ALA     1       0.300  -0.545   1.355  1.00  1.00
ATOM     11  CB  ALA     1       0.237  -0.632  -0.776  1.00  1.00
ATOM     15  CRP ALA     1       1.306   1.133   0.628  1.00  1.00
ATOM     16  OR  ALA     1       2.361   0.819   1.176  1.00  1.00
ATOM     17  NR  ALA     1       1.129   2.345   0.068  1.00  1.00
ATOM     18  HR  ALA     1       0.252   2.577  -0.315  1.00  1.00
ATOM     19  CR  ALA     1       2.150   3.364   0.108  1.00  1.00
END
REMARK X=23 Y=24 
ATOM      1  CL  ALA     1      -3.137   1.689   1.564  1.00  1.00
ATOM      5  CLP ALA     1      -1.674   1.466   1.595  1.00  1.00
ATOM      6  OL  ALA     1      -0.991   2.041   2.377  1.00  1.00
ATOM      7  NL  ALA     1      -1.178   0.640   0.664  1.00  1.00
ATOM      8  HL  ALA     1      -1.829   0.190   0.106  1.00  1.00
ATOM      9  CA  ALA     1       0.192   0.170   0.547  1.00  1.00
ATOM     10  HA  ALA     1       0.347  -0.550   1.313  1.00  1.00
ATOM     11  CB  ALA     1       0.333  -0.536  -0.821  1.00  1.00
ATOM     15  CRP ALA     1       1.325   1.194   0.686  1.00  1.00
ATOM     16  OR  ALA     1       2.348   0.906   1.293  1.00  1.00
ATOM     17  NR  ALA     1       1.165   2.398   0.103  1.00  1.00
ATOM     18  HR  ALA     1       0.311   2.617  -0.339  1.00  1.00
ATOM     19  CR  ALA     1       2.173   3.424   0.206  1.00  1.00
END
REMARK X=24 Y=25 
ATOM      1  CL  ALA     1      -3.342   1.726   1.297  1.00  1.00
ATOM      5  CLP ALA     1      -1.882   1.644   1.449  1.00  1.00
ATOM      6  OL  ALA     1      -1.296   2.423   2.124  1.00  1.00
ATOM      7  NL  ALA     1      -1.259   0.684   0.740  1.00  1.00
ATOM      8  HL  ALA     1      -1.839   0.091   0.256  1.00  1.00
ATOM      9  CA  ALA     1       0.138   0.295   0.784  1.00  1.00
ATOM     10  HA  ALA     1       0.267  -0.321   1.638  1.00  1.00
ATOM     11  CB  ALA     1       0.437  -0.541  -0.481  1.00  1.00
ATOM     15  CRP ALA     1       1.207   1.385   0.899  1.00  1.00
ATOM     16  OR  ALA     1       2.160   1.248   1.674  1.00  1.00
ATOM     17  NR  ALA     1       1.092   2.478   0.129  1.00  1.00
ATOM     18  HR  ALA     1       0.291   2.586  -0.440  1.00  1.00
ATOM     19  CR  ALA     1       2.044   3.567   0.190  1.00  1.00
END
REMARK X=25 Y=26 
ATOM      1  CL  ALA     1      -3.361   1.726   1.315  1.00  1.00
ATOM      5  CLP ALA     1      -1.890   1.687   1.423  1.00  1.00
ATOM      6  OL  ALA     1      -1.302   2.522   2.029  1.00  1.00
ATOM      7  NL  ALA     1      -1.285   0.691   0.757  1.00  1.00
ATOM      8  HL  ALA     1      -1.865   0.049   0.326  1.00  1.00
ATOM      9  CA  ALA     1       0.123   0.321   0.749  1.00  1.00
ATOM     10  HA  ALA     1       0.270  -0.331   1.585  1.00  1.00
ATOM     11  CB  ALA     1       0.408  -0.470  -0.534  1.00  1.00
ATOM     15  CRP ALA     1       1.192   1.410   0.900  1.00  1.00
ATOM     16  OR  ALA     1       2.114   1.273   1.701  1.00  1.00
ATOM     17  NR  ALA     1       1.111   2.493   0.112  1.00  1.00
ATOM     18  HR  ALA     1       0.326   2.609  -0.490  1.00  1.00
ATOM     19  CR  ALA     1       2.068   3.578   0.188  1.00  1.00
END
REMARK X=26 Y=27 
ATOM      1  CL  ALA     1      -3.419   1.747   1.251  1.00  1.00
ATOM      5  CLP ALA     1      -1.947   1.630   1.371  1.00  1.00
ATOM      6  OL  ALA     1      -1.331   2.379   2.060  1.00  1.00
ATOM      7  NL  ALA     1      -1.380   0.668   0.616  1.00  1.00
ATOM      8  HL  ALA     1      -1.992   0.115   0.104  1.00  1.00
ATOM      9  CA  ALA     1       0.007   0.227   0.571  1.00  1.00
ATOM     10  HA  ALA     1       0.086  -0.578   1.262  1.00  1.00
ATOM     11  CB  ALA     1       0.288  -0.306  -0.835  1.00  1.00
ATOM     15  CRP ALA     1       1.132   1.190   0.974  1.00  1.00
ATOM     16  OR  ALA     1       1.974   0.858   1.808  1.00  1.00
ATOM     17  NR  ALA     1       1.199   2.390   0.352  1.00  1.00
ATOM     18  HR  ALA     1       0.482   2.643  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.218   3.363   0.657  1.00  1.00
END
REMARK X=27 Y=28 
ATOM      1  CL  ALA     1      -3.430   1.748   1.261  1.00  1.00
ATOM      5  CLP ALA     1      -1.958   1.650   1.340  1.00  1.00
ATOM      6  OL  ALA     1      -1.333   2.471   1.961  1.00  1.00
ATOM      7  NL  ALA     1      -1.392   0.653   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -2.018   0.061   0.177  1.00  1.00
ATOM      9  CA  ALA     1      -0.005   0.219   0.569  1.00  1.00
ATOM     10  HA  ALA     1       0.083  -0.615   1.230  1.00  1.00
ATOM     11  CB  ALA     1       0.266  -0.275  -0.863  1.00  1.00
ATOM     15  CRP ALA     1       1.126   1.166   0.993  1.00  1.00
ATOM     16  OR  ALA     1       1.918   0.834   1.868  1.00  1.00
ATOM     17  NR  ALA     1       1.248   2.346   0.359  1.00  1.00
ATOM     18  HR  ALA     1       0.548   2.609  -0.299  1.00  1.00
ATOM     19  CR  ALA     1       2.271   3.308   0.675  1.00  1.00
END
REMARK X=28 Y=29 
ATOM      1  CL  ALA     1      -3.438   1.702   1.306  1.00  1.00
ATOM      5  CLP ALA     1      -1.962   1.659   1.317  1.00  1.00
ATOM      6  OL  ALA     1      -1.332   2.532   1.870  1.00  1.00
ATOM      7  NL  ALA     1      -1.406   0.632   0.671  1.00  1.00
ATOM      8  HL  ALA     1      -2.029   0.002   0.252  1.00  1.00
ATOM      9  CA  ALA     1      -0.007   0.228   0.554  1.00  1.00
ATOM     10  HA  ALA     1       0.103  -0.631   1.184  1.00  1.00
ATOM     11  CB  ALA     1       0.255  -0.224  -0.899  1.00  1.00
ATOM     15  CRP ALA     1       1.124   1.169   1.002  1.00  1.00
ATOM     16  OR  ALA     1       1.889   0.829   1.901  1.00  1.00
ATOM     17  NR  ALA     1       1.265   2.342   0.365  1.00  1.00
ATOM     18  HR  ALA     1       0.590   2.614  -0.306  1.00  1.00
ATOM     19  CR  ALA     1       2.313   3.280   0.698  1.00  1.00
END
REMARK X=29 Y=30 
ATOM      1  CL  ALA     1      -3.441   1.677   1.342  1.00  1.00
ATOM      5  CLP ALA     1      -1.971   1.666   1.304  1.00  1.00
ATOM      6  OL  ALA     1      -1.348   2.594   1.774  1.00  1.00
ATOM      7  NL  ALA     1      -1.408   0.602   0.696  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.062   0.329  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.235   0.538  1.00  1.00
ATOM     10  HA  ALA     1       0.114  -0.660   1.127  1.00  1.00
ATOM     11  CB  ALA     1       0.223  -0.161  -0.935  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.153   1.020  1.00  1.00
ATOM     16  OR  ALA     1       1.857   0.813   1.931  1.00  1.00
ATOM     17  NR  ALA     1       1.290   2.335   0.385  1.00  1.00
ATOM     18  HR  ALA     1       0.632   2.617  -0.298  1.00  1.00
ATOM     19  CR  ALA     1       2.337   3.252   0.749  1.00  1.00
END
REMARK X=30 Y=31 
ATOM      1  CL  ALA     1      -3.443   1.670   1.352  1.00  1.00
ATOM      5  CLP ALA     1      -1.973   1.670   1.295  1.00  1.00
ATOM      6  OL  ALA     1      -1.351   2.609   1.744  1.00  1.00
ATOM      7  NL  ALA     1      -1.409   0.597   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.076   0.355  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.237   0.533  1.00  1.00
ATOM     10  HA  ALA     1       0.119  -0.663   1.113  1.00  1.00
ATOM     11  CB  ALA     1       0.217  -0.147  -0.945  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.152   1.023  1.00  1.00
ATOM     16  OR  ALA     1       1.849   0.808   1.938  1.00  1.00
ATOM     17  NR  ALA     1       1.296   2.334   0.388  1.00  1.00
ATOM     18  HR  ALA     1       0.638   2.620  -0.293  1.00  1.00
ATOM     19  CR  ALA     1       2.342   3.249   0.754  1.00  1.00
END
REMARK X=31 Y=32 
ATOM      1  CL  ALA     1      -3.451   1.630   1.422  1.00  1.00
ATOM      5  CLP ALA     1      -1.983   1.689   1.248  1.00  1.00
ATOM      6  OL  ALA     1      -1.374   2.689   1.550  1.00  1.00
ATOM      7  NL  ALA     1      -1.421   0.569   0.756  1.00  1.00
ATOM      8  HL  ALA     1      -2.045  -0.151   0.513  1.00  1.00
ATOM      9  CA  ALA     1      -0.017   0.248   0.499  1.00  1.00
ATOM     10  HA  ALA     1       0.149  -0.681   1.023  1.00  1.00
ATOM     11  CB  ALA     1       0.171  -0.057  -0.999  1.00  1.00
ATOM     15  CRP ALA     1       1.111   1.147   1.033  1.00  1.00
ATOM     16  OR  ALA     1       1.807   0.781   1.969  1.00  1.00
ATOM     17  NR  ALA     1       1.327   2.329   0.410  1.00  1.00
ATOM     18  HR  ALA     1       0.679   2.635  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.372   3.237   0.799  1.00  1.00
END
REMARK X=32 Y=33 
ATOM      1  CL  ALA     1      -3.331   1.449   1.617  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.399   1.408  1.00  1.00
ATOM      6  OL  ALA     1      -1.169   2.255   1.904  1.00  1.00
ATOM      7  NL  ALA     1      -1.424   0.371   0.676  1.00  1.00
ATOM      8  HL  ALA     1      -2.118  -0.203   0.289  1.00  1.00
ATOM      9  CA  ALA     1      -0.062   0.001   0.310  1.00  1.00
ATOM     10  HA  ALA     1      -0.008  -1.054   0.497  1.00  1.00
ATOM     11  CB  ALA     1       0.131   0.162  -1.216  1.00  1.00
ATOM     15  CRP ALA     1       1.142   0.546   1.099  1.00  1.00
ATOM     16  OR  ALA     1       1.741  -0.171   1.894  1.00  1.00
ATOM     17  NR  ALA     1       1.537   1.815   0.864  1.00  1.00
ATOM     18  HR  ALA     1       0.963   2.391   0.297  1.00  1.00
ATOM     19  CR  ALA     1       2.669   2.426   1.513  1.00  1.00
END
REMARK X=33 Y=34 
ATOM      1  CL  ALA     1      -3.321   1.436   1.650  1.00  1.00
ATOM      5  CLP ALA     1      -1.870   1.422   1.372  1.00  1.00
ATOM      6  OL  ALA     1      -1.182   2.323   1.789  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.347   0.697  1.00  1.00
ATOM      8  HL  ALA     1      -2.106  -0.263   0.374  1.00  1.00
ATOM      9  CA  ALA     1      -0.057   0.008   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.002  -1.051   0.446  1.00  1.00
ATOM     11  CB  ALA     1       0.113   0.213  -1.212  1.00  1.00
ATOM     15  CRP ALA     1       1.139   0.538   1.102  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.196   1.881  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.803   0.879  1.00  1.00
ATOM     18  HR  ALA     1       0.972   2.397   0.326  1.00  1.00
ATOM     19  CR  ALA     1       2.672   2.407   1.539  1.00  1.00
END
REMARK X=34 Y=35 
ATOM      1  CL  ALA     1      -3.318   1.434   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -1.871   1.426   1.363  1.00  1.00
ATOM      6  OL  ALA     1      -1.186   2.341   1.756  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.343   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.101  -0.279   0.398  1.00  1.00
ATOM      9  CA  ALA     1      -0.058   0.010   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.005  -1.051   0.433  1.00  1.00
ATOM     11  CB  ALA     1       0.109   0.227  -1.215  1.00  1.00
ATOM     15  CRP ALA     1       1.138   0.536   1.100  1.00  1.00
ATOM     16  OR  ALA     1       1.723  -0.202   1.878  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.802   0.887  1.00  1.00
ATOM     18  HR  ALA     1       0.970   2.398   0.335  1.00  1.00
ATOM     19  CR  ALA     1       2.675   2.402   1.547  1.00  1.00
END
REMARK X=35 Y=36 
ATOM      1  CL  ALA     1      -3.297   1.417   1.700  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.437   1.310  1.00  1.00
ATOM      6  OL  ALA     1      -1.214   2.432   1.560  1.00  1.00
ATOM      7  NL  ALA     1      -1.412   0.320   0.746  1.00  1.00
ATOM      8  HL  ALA     1      -2.060  -0.372   0.544  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.025   0.282  1.00  1.00
ATOM     10  HA  ALA     1       0.023  -1.051   0.357  1.00  1.00
ATOM     11  CB  ALA     1       0.071   0.308  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.141   0.510   1.103  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.245   1.863  1.00  1.00
ATOM     17  NR  ALA     1       1.541   1.794   0.938  1.00  1.00
ATOM     18  HR  ALA     1       0.957   2.397   0.401  1.00  1.00
ATOM     19  CR  ALA     1       2.683   2.371   1.604  1.00  1.00
END
REMARK X=36 Y=37 
ATOM      1  CL  ALA     1      -3.283   1.421   1.730  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.449   1.277  1.00  1.00
ATOM      6  OL  ALA     1      -1.222   2.476   1.436  1.00  1.00
ATOM      7  NL  ALA     1      -1.405   0.299   0.773  1.00  1.00
ATOM      8  HL  ALA     1      -2.034  -0.422   0.640  1.00  1.00
ATOM      9  CA  ALA     1      -0.063   0.028   0.272  1.00  1.00
ATOM     10  HA  ALA     1       0.015  -1.050   0.307  1.00  1.00
ATOM     11  CB  ALA     1       0.057   0.364  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.134   0.492   1.093  1.00  1.00
ATOM     16  OR  ALA     1       1.729  -0.288   1.825  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.779   0.976  1.00  1.00
ATOM     18  HR  ALA     1       0.945   2.388   0.456  1.00  1.00
ATOM     19  CR  ALA     1       2.682   2.335   1.653  1.00  1.00
END
REMARK X=37 Y=38 
ATOM      1  CL  ALA     1      -3.265   1.435   1.760  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.457   1.257  1.00  1.00
ATOM      6  OL  ALA     1      -1.229   2.500   1.343  1.00  1.00
ATOM      7  NL  ALA     1      -1.398   0.292   0.802  1.00  1.00
ATOM      8  HL  ALA     1      -2.014  -0.454   0.728  1.00  1.00
ATOM      9  CA  ALA     1      -0.067   0.024   0.264  1.00  1.00
ATOM     10  HA  ALA     1       0.011  -1.049   0.257  1.00  1.00
ATOM     11  CB  ALA     1       0.028   0.426  -1.206  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.464   1.092  1.00  1.00
ATOM     16  OR  ALA     1       1.748  -0.346   1.781  1.00  1.00
ATOM     17  NR  ALA     1       1.532   1.754   1.029  1.00  1.00
ATOM     18  HR  ALA     1       0.931   2.385   0.536  1.00  1.00
ATOM     19  CR  ALA     1       2.676   2.280   1.721  1.00  1.00
END
REMARK X=38 Y=39 
ATOM      1  CL  ALA     1      -3.236   1.453   1.772  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.473   1.217  1.00  1.00
ATOM      6  OL  ALA     1      -1.244   2.522   1.222  1.00  1.00
ATOM      7  NL  ALA     1      -1.388   0.292   0.824  1.00  1.00
ATOM      8  HL  ALA     1      -1.982  -0.485   0.827  1.00  1.00
ATOM      9  CA  ALA     1      -0.066   0.031   0.248  1.00  1.00
ATOM     10  HA  ALA     1       0.018  -1.048   0.230  1.00  1.00
ATOM     11  CB  ALA     1       0.011   0.464  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.452   1.088  1.00  1.00
ATOM     16  OR  ALA     1       1.767  -0.373   1.737  1.00  1.00
ATOM     17  NR  ALA     1       1.517   1.749   1.061  1.00  1.00
ATOM     18  HR  ALA     1       0.906   2.387   0.586  1.00  1.00
ATOM     19  CR  ALA     1       2.660   2.262   1.754  1.00  1.00
END
REMARK X=39 Y=40 
ATOM      1  CL  ALA     1      -3.225   1.461   1.784  1.00  1.00
ATOM      5  CLP ALA     1      -1.878   1.466   1.191  1.00  1.00
ATOM      6  OL  ALA     1      -1.276   2.527   1.106  1.00  1.00
ATOM      7  NL  ALA     1      -1.375   0.274   0.839  1.00  1.00
ATOM      8  HL  ALA     1      -1.947  -0.517   0.921  1.00  1.00
ATOM      9  CA  ALA     1      -0.077   0.024   0.236  1.00  1.00
ATOM     10  HA  ALA     1       0.009  -1.048   0.194  1.00  1.00
ATOM     11  CB  ALA     1      -0.004   0.503  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.436   1.066  1.00  1.00
ATOM     16  OR  ALA     1       1.800  -0.403   1.678  1.00  1.00
ATOM     17  NR  ALA     1       1.483   1.736   1.091  1.00  1.00
ATOM     18  HR  ALA     1       0.861   2.388   0.647  1.00  1.00
ATOM     19  CR  ALA     1       2.642   2.246   1.792  1.00  1.00
END
REMARK X=40 Y=41 
ATOM      1  CL  ALA     1      -3.212   1.465   1.797  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.470   1.168  1.00  1.00
ATOM      6  OL  ALA     1      -1.286   2.526   1.008  1.00  1.00
ATOM      7  NL  ALA     1      -1.363   0.265   0.860  1.00  1.00
ATOM      8  HL  ALA     1      -1.914  -0.534   1.016  1.00  1.00
ATOM      9  CA  ALA     1      -0.074   0.012   0.232  1.00  1.00
ATOM     10  HA  ALA     1       0.001  -1.058   0.173  1.00  1.00
ATOM     11  CB  ALA     1      -0.020   0.528  -1.210  1.00  1.00
ATOM     15  CRP ALA     1       1.147   0.408   1.060  1.00  1.00
ATOM     16  OR  ALA     1       1.827  -0.445   1.625  1.00  1.00
ATOM     17  NR  ALA     1       1.461   1.721   1.140  1.00  1.00
ATOM     18  HR  ALA     1       0.821   2.361   0.731  1.00  1.00
ATOM     19  CR  ALA     1       2.614   2.214   1.845  1.00  1.00
END
REMARK X=41 Y=42 
ATOM      1  CL  ALA     1      -3.185   1.487   1.790  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.480   1.139  1.00  1.00
ATOM      6  OL  ALA     1      -1.293   2.532   0.896  1.00  1.00
ATOM      7  NL  ALA     1      -1.349   0.268   0.862  1.00  1.00
ATOM      8  HL  ALA     1      -1.881  -0.527   1.095  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.013   0.226  1.00  1.00
ATOM     10  HA  ALA     1      -0.006  -1.063   0.151  1.00  1.00
ATOM     11  CB  ALA     1      -0.019   0.539  -1.224  1.00  1.00
ATOM     15  CRP ALA     1       1.170   0.398   1.031  1.00  1.00
ATOM     16  OR  ALA     1       1.871  -0.463   1.540  1.00  1.00
ATOM     17  NR  ALA     1       1.447   1.706   1.159  1.00  1.00
ATOM     18  HR  ALA     1       0.788   2.362   0.800  1.00  1.00
ATOM     19  CR  ALA     1       2.602   2.205   1.868  1.00  1.00
END
REMARK X=42 Y=43 
ATOM      1  CL  ALA     1      -3.257   1.605   1.105  1.00  1.00
ATOM      5  CLP ALA     1      -1.941   1.459   0.447  1.00  1.00
ATOM      6  OL  ALA     1      -1.481   2.369  -0.223  1.00  1.00
ATOM      7  NL  ALA     1      -1.303   0.291   0.647  1.00  1.00
ATOM      8  HL  ALA     1      -1.743  -0.379   1.229  1.00  1.00
ATOM      9  CA  ALA     1      -0.011  -0.077   0.099  1.00  1.00
ATOM     10  HA  ALA     1       0.155  -1.099   0.417  1.00  1.00
ATOM     11  CB  ALA     1       0.001  -0.097  -1.439  1.00  1.00
ATOM     15  CRP ALA     1       1.191   0.673   0.683  1.00  1.00
ATOM     16  OR  ALA     1       2.015   0.103   1.375  1.00  1.00
ATOM     17  NR  ALA     1       1.303   1.983   0.393  1.00  1.00
ATOM     18  HR  ALA     1       0.553   2.411  -0.109  1.00  1.00
ATOM     19  CR  ALA     1       2.395   2.811   0.843  1.00  1.00
END
FIXED
  
rmsd: RMSDCalculate the RMSD with respect to a reference structure. This action is a shortcut and uses the defaults shown here. More details SQUARED  This should be setted if you want MSD instead of RMSD  TYPE the manner in which RMSD alignment is performed=OPTIMAL REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=
regtest/trajectories/path_msd/allv.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/trajectories/path_msd/allv.pdb
    
REMARK X=1 Y=2 
ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00
ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00
ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00
ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00
ATOM      8  HL  ALA     1      -1.845   0.961  -0.011  1.00  1.00
ATOM      9  CA  ALA     1      -0.003  -0.019   0.021  1.00  1.00
ATOM     10  HA  ALA     1       0.205  -1.051   0.259  1.00  1.00
ATOM     11  CB  ALA     1       0.009   0.135  -1.509  1.00  1.00
ATOM     15  CRP ALA     1       1.121   0.799   0.663  1.00  1.00
ATOM     16  OR  ALA     1       1.723   1.669   0.043  1.00  1.00
ATOM     17  NR  ALA     1       1.423   0.519   1.941  1.00  1.00
ATOM     18  HR  ALA     1       0.873  -0.161   2.413  1.00  1.00
ATOM     19  CR  ALA     1       2.477   1.187   2.675  1.00  1.00
END
FIXED
REMARK X=2 Y=3 
ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00
ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00
ATOM      6  OL  ALA     1      -1.201  -0.849   2.425  1.00  1.00
ATOM      7  NL  ALA     1      -1.296   0.337   0.534  1.00  1.00
ATOM      8  HL  ALA     1      -1.807   0.951  -0.044  1.00  1.00
ATOM      9  CA  ALA     1       0.009  -0.067   0.033  1.00  1.00
ATOM     10  HA  ALA     1       0.175  -1.105   0.283  1.00  1.00
ATOM     11  CB  ALA     1       0.027   0.046  -1.501  1.00  1.00
ATOM     15  CRP ALA     1       1.149   0.725   0.654  1.00  1.00
ATOM     16  OR  ALA     1       1.835   1.491  -0.011  1.00  1.00
ATOM     17  NR  ALA     1       1.380   0.537   1.968  1.00  1.00
ATOM     18  HR  ALA     1       0.764  -0.060   2.461  1.00  1.00
ATOM     19  CR  ALA     1       2.431   1.195   2.683  1.00  1.00
END
REMARK X=3 Y=4 
ATOM      1  CL  ALA     1      -2.990   0.383   2.277  1.00  1.00
ATOM      5  CLP ALA     1      -1.664  -0.085   1.831  1.00  1.00
ATOM      6  OL  ALA     1      -0.987  -0.835   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.227   0.364   0.646  1.00  1.00
ATOM      8  HL  ALA     1      -1.798   0.982   0.124  1.00  1.00
ATOM      9  CA  ALA     1       0.026  -0.028   0.044  1.00  1.00
ATOM     10  HA  ALA     1       0.224  -1.060   0.284  1.00  1.00
ATOM     11  CB  ALA     1      -0.076   0.107  -1.483  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.776   0.577  1.00  1.00
ATOM     16  OR  ALA     1       1.900   1.463  -0.158  1.00  1.00
ATOM     17  NR  ALA     1       1.494   0.666   1.888  1.00  1.00
ATOM     18  HR  ALA     1       0.882   0.122   2.437  1.00  1.00
ATOM     19  CR  ALA     1       2.580   1.341   2.529  1.00  1.00
END
REMARK X=4 Y=5 
ATOM      1  CL  ALA     1      -3.006   0.350   2.252  1.00  1.00
ATOM      5  CLP ALA     1      -1.680  -0.112   1.826  1.00  1.00
ATOM      6  OL  ALA     1      -1.025  -0.896   2.508  1.00  1.00
ATOM      7  NL  ALA     1      -1.220   0.368   0.654  1.00  1.00
ATOM      8  HL  ALA     1      -1.771   1.013   0.137  1.00  1.00
ATOM      9  CA  ALA     1       0.040  -0.029   0.062  1.00  1.00
ATOM     10  HA  ALA     1       0.210  -1.076   0.277  1.00  1.00
ATOM     11  CB  ALA     1      -0.066   0.148  -1.465  1.00  1.00
ATOM     15  CRP ALA     1       1.241   0.738   0.605  1.00  1.00
ATOM     16  OR  ALA     1       1.986   1.347  -0.125  1.00  1.00
ATOM     17  NR  ALA     1       1.446   0.694   1.940  1.00  1.00
ATOM     18  HR  ALA     1       0.796   0.210   2.481  1.00  1.00
ATOM     19  CR  ALA     1       2.544   1.350   2.582  1.00  1.00
END
REMARK X=5 Y=6 
ATOM      1  CL  ALA     1      -3.002   0.343   2.271  1.00  1.00
ATOM      5  CLP ALA     1      -1.672  -0.125   1.828  1.00  1.00
ATOM      6  OL  ALA     1      -1.028  -0.942   2.486  1.00  1.00
ATOM      7  NL  ALA     1      -1.213   0.373   0.670  1.00  1.00
ATOM      8  HL  ALA     1      -1.752   1.033   0.169  1.00  1.00
ATOM      9  CA  ALA     1       0.041  -0.032   0.055  1.00  1.00
ATOM     10  HA  ALA     1       0.201  -1.079   0.245  1.00  1.00
ATOM     11  CB  ALA     1      -0.079   0.194  -1.466  1.00  1.00
ATOM     15  CRP ALA     1       1.257   0.720   0.601  1.00  1.00
ATOM     16  OR  ALA     1       2.057   1.240  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.422   0.730   1.942  1.00  1.00
ATOM     18  HR  ALA     1       0.740   0.303   2.500  1.00  1.00
ATOM     19  CR  ALA     1       2.528   1.373   2.598  1.00  1.00
END
REMARK X=6 Y=7 
ATOM      1  CL  ALA     1      -3.144   1.457   1.417  1.00  1.00
ATOM      5  CLP ALA     1      -1.943   0.587   1.450  1.00  1.00
ATOM      6  OL  ALA     1      -1.588   0.028   2.480  1.00  1.00
ATOM      7  NL  ALA     1      -1.281   0.449   0.306  1.00  1.00
ATOM      8  HL  ALA     1      -1.578   0.914  -0.520  1.00  1.00
ATOM      9  CA  ALA     1      -0.132  -0.428   0.139  1.00  1.00
ATOM     10  HA  ALA     1      -0.264  -1.291   0.758  1.00  1.00
ATOM     11  CB  ALA     1      -0.066  -0.855  -1.329  1.00  1.00
ATOM     15  CRP ALA     1       1.193   0.220   0.554  1.00  1.00
ATOM     16  OR  ALA     1       2.195   0.098  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.224   0.872   1.737  1.00  1.00
ATOM     18  HR  ALA     1       0.399   0.943   2.273  1.00  1.00
ATOM     19  CR  ALA     1       2.413   1.511   2.254  1.00  1.00
END
REMARK X=7 Y=8 
ATOM      1  CL  ALA     1      -3.140   1.441   1.453  1.00  1.00
ATOM      5  CLP ALA     1      -1.944   0.576   1.465  1.00  1.00
ATOM      6  OL  ALA     1      -1.587  -0.018   2.487  1.00  1.00
ATOM      7  NL  ALA     1      -1.274   0.465   0.322  1.00  1.00
ATOM      8  HL  ALA     1      -1.571   0.957  -0.486  1.00  1.00
ATOM      9  CA  ALA     1      -0.124  -0.418   0.135  1.00  1.00
ATOM     10  HA  ALA     1      -0.274  -1.304   0.729  1.00  1.00
ATOM     11  CB  ALA     1      -0.063  -0.813  -1.347  1.00  1.00
ATOM     15  CRP ALA     1       1.201   0.199   0.572  1.00  1.00
ATOM     16  OR  ALA     1       2.227   0.007  -0.072  1.00  1.00
ATOM     17  NR  ALA     1       1.215   0.910   1.709  1.00  1.00
ATOM     18  HR  ALA     1       0.369   1.020   2.200  1.00  1.00
ATOM     19  CR  ALA     1       2.393   1.536   2.237  1.00  1.00
END
REMARK X=8 Y=9 
ATOM      1  CL  ALA     1      -3.140   1.420   1.442  1.00  1.00
ATOM      5  CLP ALA     1      -1.948   0.546   1.448  1.00  1.00
ATOM      6  OL  ALA     1      -1.618  -0.065   2.460  1.00  1.00
ATOM      7  NL  ALA     1      -1.255   0.469   0.311  1.00  1.00
ATOM      8  HL  ALA     1      -1.538   0.979  -0.490  1.00  1.00
ATOM      9  CA  ALA     1      -0.107  -0.412   0.124  1.00  1.00
ATOM     10  HA  ALA     1      -0.257  -1.312   0.685  1.00  1.00
ATOM     11  CB  ALA     1      -0.028  -0.770  -1.375  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.186   0.600  1.00  1.00
ATOM     16  OR  ALA     1       2.269  -0.069   0.026  1.00  1.00
ATOM     17  NR  ALA     1       1.193   0.966   1.687  1.00  1.00
ATOM     18  HR  ALA     1       0.333   1.114   2.120  1.00  1.00
ATOM     19  CR  ALA     1       2.377   1.589   2.240  1.00  1.00
END
REMARK X=9 Y=10 
ATOM      1  CL  ALA     1      -3.110   1.698   0.880  1.00  1.00
ATOM      5  CLP ALA     1      -2.021   0.734   1.142  1.00  1.00
ATOM      6  OL  ALA     1      -1.859   0.257   2.258  1.00  1.00
ATOM      7  NL  ALA     1      -1.229   0.414   0.114  1.00  1.00
ATOM      8  HL  ALA     1      -1.371   0.826  -0.771  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.593   0.188  1.00  1.00
ATOM     10  HA  ALA     1      -0.481  -1.374   0.851  1.00  1.00
ATOM     11  CB  ALA     1       0.011  -1.180  -1.220  1.00  1.00
ATOM     15  CRP ALA     1       1.163  -0.060   0.716  1.00  1.00
ATOM     16  OR  ALA     1       2.227  -0.564   0.393  1.00  1.00
ATOM     17  NR  ALA     1       1.127   0.960   1.594  1.00  1.00
ATOM     18  HR  ALA     1       0.234   1.295   1.847  1.00  1.00
ATOM     19  CR  ALA     1       2.303   1.549   2.172  1.00  1.00
END
REMARK X=10 Y=11 
ATOM      1  CL  ALA     1      -3.139   1.652   0.924  1.00  1.00
ATOM      5  CLP ALA     1      -2.039   0.698   1.169  1.00  1.00
ATOM      6  OL  ALA     1      -1.868   0.201   2.278  1.00  1.00
ATOM      7  NL  ALA     1      -1.239   0.411   0.139  1.00  1.00
ATOM      8  HL  ALA     1      -1.385   0.842  -0.737  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.574   0.193  1.00  1.00
ATOM     10  HA  ALA     1      -0.477  -1.381   0.833  1.00  1.00
ATOM     11  CB  ALA     1       0.029  -1.142  -1.231  1.00  1.00
ATOM     15  CRP ALA     1       1.162  -0.048   0.731  1.00  1.00
ATOM     16  OR  ALA     1       2.220  -0.597   0.472  1.00  1.00
ATOM     17  NR  ALA     1       1.122   1.024   1.537  1.00  1.00
ATOM     18  HR  ALA     1       0.233   1.395   1.752  1.00  1.00
ATOM     19  CR  ALA     1       2.300   1.629   2.102  1.00  1.00
END
REMARK X=11 Y=12 
ATOM      1  CL  ALA     1      -3.706   1.088   0.468  1.00  1.00
ATOM      5  CLP ALA     1      -2.458   0.598   1.082  1.00  1.00
ATOM      6  OL  ALA     1      -2.390   0.404   2.277  1.00  1.00
ATOM      7  NL  ALA     1      -1.427   0.382   0.258  1.00  1.00
ATOM      8  HL  ALA     1      -1.513   0.559  -0.713  1.00  1.00
ATOM      9  CA  ALA     1      -0.157  -0.192   0.685  1.00  1.00
ATOM     10  HA  ALA     1      -0.343  -0.912   1.470  1.00  1.00
ATOM     11  CB  ALA     1       0.462  -0.936  -0.512  1.00  1.00
ATOM     15  CRP ALA     1       0.840   0.814   1.241  1.00  1.00
ATOM     16  OR  ALA     1       2.034   0.549   1.354  1.00  1.00
ATOM     17  NR  ALA     1       0.368   2.017   1.650  1.00  1.00
ATOM     18  HR  ALA     1      -0.613   2.169   1.589  1.00  1.00
ATOM     19  CR  ALA     1       1.215   3.044   2.195  1.00  1.00
END
REMARK X=12 Y=13 
ATOM      1  CL  ALA     1      -3.699   1.173   0.487  1.00  1.00
ATOM      5  CLP ALA     1      -2.464   0.631   1.079  1.00  1.00
ATOM      6  OL  ALA     1      -2.402   0.386   2.275  1.00  1.00
ATOM      7  NL  ALA     1      -1.434   0.437   0.260  1.00  1.00
ATOM      8  HL  ALA     1      -1.516   0.652  -0.701  1.00  1.00
ATOM      9  CA  ALA     1      -0.174  -0.174   0.667  1.00  1.00
ATOM     10  HA  ALA     1      -0.377  -0.924   1.411  1.00  1.00
ATOM     11  CB  ALA     1       0.451  -0.859  -0.570  1.00  1.00
ATOM     15  CRP ALA     1       0.839   0.801   1.280  1.00  1.00
ATOM     16  OR  ALA     1       1.999   0.474   1.468  1.00  1.00
ATOM     17  NR  ALA     1       0.404   2.024   1.627  1.00  1.00
ATOM     18  HR  ALA     1      -0.565   2.225   1.505  1.00  1.00
ATOM     19  CR  ALA     1       1.262   3.025   2.214  1.00  1.00
END
REMARK X=13 Y=14 
ATOM      1  CL  ALA     1      -3.653   0.990   1.121  1.00  1.00
ATOM      5  CLP ALA     1      -2.321   0.364   1.249  1.00  1.00
ATOM      6  OL  ALA     1      -2.006  -0.222   2.265  1.00  1.00
ATOM      7  NL  ALA     1      -1.498   0.501   0.205  1.00  1.00
ATOM      8  HL  ALA     1      -1.794   0.978  -0.603  1.00  1.00
ATOM      9  CA  ALA     1      -0.190  -0.127   0.128  1.00  1.00
ATOM     10  HA  ALA     1      -0.216  -1.086   0.627  1.00  1.00
ATOM     11  CB  ALA     1       0.159  -0.359  -1.359  1.00  1.00
ATOM     15  CRP ALA     1       0.933   0.668   0.793  1.00  1.00
ATOM     16  OR  ALA     1       2.107   0.313   0.705  1.00  1.00
ATOM     17  NR  ALA     1       0.604   1.770   1.498  1.00  1.00
ATOM     18  HR  ALA     1      -0.359   1.986   1.593  1.00  1.00
ATOM     19  CR  ALA     1       1.573   2.595   2.158  1.00  1.00
END
REMARK X=14 Y=15 
ATOM      1  CL  ALA     1      -3.641   0.954   1.179  1.00  1.00
ATOM      5  CLP ALA     1      -2.294   0.335   1.290  1.00  1.00
ATOM      6  OL  ALA     1      -1.964  -0.273   2.288  1.00  1.00
ATOM      7  NL  ALA     1      -1.485   0.499   0.235  1.00  1.00
ATOM      8  HL  ALA     1      -1.803   0.995  -0.564  1.00  1.00
ATOM      9  CA  ALA     1      -0.175  -0.118   0.130  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.077   0.601  1.00  1.00
ATOM     11  CB  ALA     1       0.162  -0.300  -1.355  1.00  1.00
ATOM     15  CRP ALA     1       0.952   0.671   0.815  1.00  1.00
ATOM     16  OR  ALA     1       2.104   0.260   0.791  1.00  1.00
ATOM     17  NR  ALA     1       0.633   1.808   1.450  1.00  1.00
ATOM     18  HR  ALA     1      -0.328   2.065   1.503  1.00  1.00
ATOM     19  CR  ALA     1       1.608   2.627   2.129  1.00  1.00
END
REMARK X=15 Y=16 
ATOM      1  CL  ALA     1      -3.635   0.925   1.244  1.00  1.00
ATOM      5  CLP ALA     1      -2.297   0.305   1.309  1.00  1.00
ATOM      6  OL  ALA     1      -1.941  -0.334   2.290  1.00  1.00
ATOM      7  NL  ALA     1      -1.500   0.490   0.251  1.00  1.00
ATOM      8  HL  ALA     1      -1.827   1.009  -0.537  1.00  1.00
ATOM      9  CA  ALA     1      -0.178  -0.110   0.119  1.00  1.00
ATOM     10  HA  ALA     1      -0.205  -1.094   0.536  1.00  1.00
ATOM     11  CB  ALA     1       0.147  -0.217  -1.379  1.00  1.00
ATOM     15  CRP ALA     1       0.943   0.643   0.832  1.00  1.00
ATOM     16  OR  ALA     1       2.074   0.198   0.871  1.00  1.00
ATOM     17  NR  ALA     1       0.637   1.821   1.423  1.00  1.00
ATOM     18  HR  ALA     1      -0.311   2.123   1.418  1.00  1.00
ATOM     19  CR  ALA     1       1.602   2.629   2.109  1.00  1.00
END
REMARK X=16 Y=17 
ATOM      1  CL  ALA     1      -3.632   0.856   1.331  1.00  1.00
ATOM      5  CLP ALA     1      -2.282   0.250   1.355  1.00  1.00
ATOM      6  OL  ALA     1      -1.906  -0.403   2.301  1.00  1.00
ATOM      7  NL  ALA     1      -1.515   0.478   0.275  1.00  1.00
ATOM      8  HL  ALA     1      -1.860   0.990  -0.485  1.00  1.00
ATOM      9  CA  ALA     1      -0.192  -0.105   0.098  1.00  1.00
ATOM     10  HA  ALA     1      -0.204  -1.121   0.473  1.00  1.00
ATOM     11  CB  ALA     1       0.129  -0.136  -1.408  1.00  1.00
ATOM     15  CRP ALA     1       0.931   0.615   0.844  1.00  1.00
ATOM     16  OR  ALA     1       2.043   0.122   0.934  1.00  1.00
ATOM     17  NR  ALA     1       0.651   1.819   1.388  1.00  1.00
ATOM     18  HR  ALA     1      -0.283   2.155   1.349  1.00  1.00
ATOM     19  CR  ALA     1       1.624   2.595   2.115  1.00  1.00
END
REMARK X=17 Y=18 
ATOM      1  CL  ALA     1      -3.628   0.823   1.358  1.00  1.00
ATOM      5  CLP ALA     1      -2.277   0.241   1.370  1.00  1.00
ATOM      6  OL  ALA     1      -1.871  -0.396   2.325  1.00  1.00
ATOM      7  NL  ALA     1      -1.525   0.469   0.284  1.00  1.00
ATOM      8  HL  ALA     1      -1.898   0.970  -0.482  1.00  1.00
ATOM      9  CA  ALA     1      -0.195  -0.094   0.086  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.122   0.423  1.00  1.00
ATOM     11  CB  ALA     1       0.146  -0.058  -1.413  1.00  1.00
ATOM     15  CRP ALA     1       0.919   0.599   0.874  1.00  1.00
ATOM     16  OR  ALA     1       1.997   0.065   1.039  1.00  1.00
ATOM     17  NR  ALA     1       0.655   1.830   1.373  1.00  1.00
ATOM     18  HR  ALA     1      -0.248   2.200   1.261  1.00  1.00
ATOM     19  CR  ALA     1       1.625   2.581   2.124  1.00  1.00
END
REMARK X=18 Y=19 
ATOM      1  CL  ALA     1      -3.539   0.055   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -2.117  -0.208   1.378  1.00  1.00
ATOM      6  OL  ALA     1      -1.453  -0.902   2.125  1.00  1.00
ATOM      7  NL  ALA     1      -1.602   0.351   0.289  1.00  1.00
ATOM      8  HL  ALA     1      -2.185   0.875  -0.310  1.00  1.00
ATOM      9  CA  ALA     1      -0.243   0.129  -0.186  1.00  1.00
ATOM     10  HA  ALA     1      -0.041  -0.924  -0.159  1.00  1.00
ATOM     11  CB  ALA     1      -0.153   0.625  -1.651  1.00  1.00
ATOM     15  CRP ALA     1       0.852   0.806   0.637  1.00  1.00
ATOM     16  OR  ALA     1       2.007   0.400   0.594  1.00  1.00
ATOM     17  NR  ALA     1       0.508   1.855   1.401  1.00  1.00
ATOM     18  HR  ALA     1      -0.445   2.112   1.454  1.00  1.00
ATOM     19  CR  ALA     1       1.460   2.569   2.226  1.00  1.00
END
REMARK X=19 Y=20 
ATOM      1  CL  ALA     1      -3.578   0.084   1.603  1.00  1.00
ATOM      5  CLP ALA     1      -2.140  -0.156   1.375  1.00  1.00
ATOM      6  OL  ALA     1      -1.473  -0.732   2.197  1.00  1.00
ATOM      7  NL  ALA     1      -1.623   0.335   0.237  1.00  1.00
ATOM      8  HL  ALA     1      -2.220   0.753  -0.416  1.00  1.00
ATOM      9  CA  ALA     1      -0.253   0.120  -0.195  1.00  1.00
ATOM     10  HA  ALA     1      -0.048  -0.931  -0.153  1.00  1.00
ATOM     11  CB  ALA     1      -0.128   0.612  -1.663  1.00  1.00
ATOM     15  CRP ALA     1       0.823   0.801   0.637  1.00  1.00
ATOM     16  OR  ALA     1       1.969   0.367   0.665  1.00  1.00
ATOM     17  NR  ALA     1       0.477   1.912   1.333  1.00  1.00
ATOM     18  HR  ALA     1      -0.468   2.199   1.317  1.00  1.00
ATOM     19  CR  ALA     1       1.410   2.627   2.163  1.00  1.00
END
REMARK X=20 Y=21 
ATOM      1  CL  ALA     1      -3.113   1.661   1.504  1.00  1.00
ATOM      5  CLP ALA     1      -1.769   1.059   1.566  1.00  1.00
ATOM      6  OL  ALA     1      -1.201   0.940   2.629  1.00  1.00
ATOM      7  NL  ALA     1      -1.219   0.714   0.392  1.00  1.00
ATOM      8  HL  ALA     1      -1.742   0.797  -0.435  1.00  1.00
ATOM      9  CA  ALA     1       0.058   0.023   0.242  1.00  1.00
ATOM     10  HA  ALA     1      -0.001  -0.896   0.782  1.00  1.00
ATOM     11  CB  ALA     1       0.235  -0.295  -1.249  1.00  1.00
ATOM     15  CRP ALA     1       1.299   0.757   0.745  1.00  1.00
ATOM     16  OR  ALA     1       2.276   0.138   1.135  1.00  1.00
ATOM     17  NR  ALA     1       1.277   2.102   0.736  1.00  1.00
ATOM     18  HR  ALA     1       0.447   2.567   0.458  1.00  1.00
ATOM     19  CR  ALA     1       2.391   2.896   1.191  1.00  1.00
END
REMARK X=21 Y=22 
ATOM      1  CL  ALA     1      -3.089   1.850   1.546  1.00  1.00
ATOM      5  CLP ALA     1      -1.667   1.457   1.629  1.00  1.00
ATOM      6  OL  ALA     1      -0.974   1.868   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.204   0.683   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -1.844   0.360  -0.021  1.00  1.00
ATOM      9  CA  ALA     1       0.126   0.105   0.564  1.00  1.00
ATOM     10  HA  ALA     1       0.239  -0.555   1.391  1.00  1.00
ATOM     11  CB  ALA     1       0.215  -0.722  -0.739  1.00  1.00
ATOM     15  CRP ALA     1       1.311   1.068   0.623  1.00  1.00
ATOM     16  OR  ALA     1       2.369   0.726   1.149  1.00  1.00
ATOM     17  NR  ALA     1       1.156   2.292   0.077  1.00  1.00
ATOM     18  HR  ALA     1       0.273   2.549  -0.285  1.00  1.00
ATOM     19  CR  ALA     1       2.201   3.277   0.107  1.00  1.00
END
REMARK X=22 Y=23 
ATOM      1  CL  ALA     1      -3.102   1.775   1.619  1.00  1.00
ATOM      5  CLP ALA     1      -1.661   1.466   1.659  1.00  1.00
ATOM      6  OL  ALA     1      -0.945   1.961   2.476  1.00  1.00
ATOM      7  NL  ALA     1      -1.205   0.663   0.688  1.00  1.00
ATOM      8  HL  ALA     1      -1.854   0.269   0.091  1.00  1.00
ATOM      9  CA  ALA     1       0.147   0.134   0.561  1.00  1.00
ATOM     10  HA  ALA     1       0.300  -0.545   1.355  1.00  1.00
ATOM     11  CB  ALA     1       0.237  -0.632  -0.776  1.00  1.00
ATOM     15  CRP ALA     1       1.306   1.133   0.628  1.00  1.00
ATOM     16  OR  ALA     1       2.361   0.819   1.176  1.00  1.00
ATOM     17  NR  ALA     1       1.129   2.345   0.068  1.00  1.00
ATOM     18  HR  ALA     1       0.252   2.577  -0.315  1.00  1.00
ATOM     19  CR  ALA     1       2.150   3.364   0.108  1.00  1.00
END
REMARK X=23 Y=24 
ATOM      1  CL  ALA     1      -3.137   1.689   1.564  1.00  1.00
ATOM      5  CLP ALA     1      -1.674   1.466   1.595  1.00  1.00
ATOM      6  OL  ALA     1      -0.991   2.041   2.377  1.00  1.00
ATOM      7  NL  ALA     1      -1.178   0.640   0.664  1.00  1.00
ATOM      8  HL  ALA     1      -1.829   0.190   0.106  1.00  1.00
ATOM      9  CA  ALA     1       0.192   0.170   0.547  1.00  1.00
ATOM     10  HA  ALA     1       0.347  -0.550   1.313  1.00  1.00
ATOM     11  CB  ALA     1       0.333  -0.536  -0.821  1.00  1.00
ATOM     15  CRP ALA     1       1.325   1.194   0.686  1.00  1.00
ATOM     16  OR  ALA     1       2.348   0.906   1.293  1.00  1.00
ATOM     17  NR  ALA     1       1.165   2.398   0.103  1.00  1.00
ATOM     18  HR  ALA     1       0.311   2.617  -0.339  1.00  1.00
ATOM     19  CR  ALA     1       2.173   3.424   0.206  1.00  1.00
END
REMARK X=24 Y=25 
ATOM      1  CL  ALA     1      -3.342   1.726   1.297  1.00  1.00
ATOM      5  CLP ALA     1      -1.882   1.644   1.449  1.00  1.00
ATOM      6  OL  ALA     1      -1.296   2.423   2.124  1.00  1.00
ATOM      7  NL  ALA     1      -1.259   0.684   0.740  1.00  1.00
ATOM      8  HL  ALA     1      -1.839   0.091   0.256  1.00  1.00
ATOM      9  CA  ALA     1       0.138   0.295   0.784  1.00  1.00
ATOM     10  HA  ALA     1       0.267  -0.321   1.638  1.00  1.00
ATOM     11  CB  ALA     1       0.437  -0.541  -0.481  1.00  1.00
ATOM     15  CRP ALA     1       1.207   1.385   0.899  1.00  1.00
ATOM     16  OR  ALA     1       2.160   1.248   1.674  1.00  1.00
ATOM     17  NR  ALA     1       1.092   2.478   0.129  1.00  1.00
ATOM     18  HR  ALA     1       0.291   2.586  -0.440  1.00  1.00
ATOM     19  CR  ALA     1       2.044   3.567   0.190  1.00  1.00
END
REMARK X=25 Y=26 
ATOM      1  CL  ALA     1      -3.361   1.726   1.315  1.00  1.00
ATOM      5  CLP ALA     1      -1.890   1.687   1.423  1.00  1.00
ATOM      6  OL  ALA     1      -1.302   2.522   2.029  1.00  1.00
ATOM      7  NL  ALA     1      -1.285   0.691   0.757  1.00  1.00
ATOM      8  HL  ALA     1      -1.865   0.049   0.326  1.00  1.00
ATOM      9  CA  ALA     1       0.123   0.321   0.749  1.00  1.00
ATOM     10  HA  ALA     1       0.270  -0.331   1.585  1.00  1.00
ATOM     11  CB  ALA     1       0.408  -0.470  -0.534  1.00  1.00
ATOM     15  CRP ALA     1       1.192   1.410   0.900  1.00  1.00
ATOM     16  OR  ALA     1       2.114   1.273   1.701  1.00  1.00
ATOM     17  NR  ALA     1       1.111   2.493   0.112  1.00  1.00
ATOM     18  HR  ALA     1       0.326   2.609  -0.490  1.00  1.00
ATOM     19  CR  ALA     1       2.068   3.578   0.188  1.00  1.00
END
REMARK X=26 Y=27 
ATOM      1  CL  ALA     1      -3.419   1.747   1.251  1.00  1.00
ATOM      5  CLP ALA     1      -1.947   1.630   1.371  1.00  1.00
ATOM      6  OL  ALA     1      -1.331   2.379   2.060  1.00  1.00
ATOM      7  NL  ALA     1      -1.380   0.668   0.616  1.00  1.00
ATOM      8  HL  ALA     1      -1.992   0.115   0.104  1.00  1.00
ATOM      9  CA  ALA     1       0.007   0.227   0.571  1.00  1.00
ATOM     10  HA  ALA     1       0.086  -0.578   1.262  1.00  1.00
ATOM     11  CB  ALA     1       0.288  -0.306  -0.835  1.00  1.00
ATOM     15  CRP ALA     1       1.132   1.190   0.974  1.00  1.00
ATOM     16  OR  ALA     1       1.974   0.858   1.808  1.00  1.00
ATOM     17  NR  ALA     1       1.199   2.390   0.352  1.00  1.00
ATOM     18  HR  ALA     1       0.482   2.643  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.218   3.363   0.657  1.00  1.00
END
REMARK X=27 Y=28 
ATOM      1  CL  ALA     1      -3.430   1.748   1.261  1.00  1.00
ATOM      5  CLP ALA     1      -1.958   1.650   1.340  1.00  1.00
ATOM      6  OL  ALA     1      -1.333   2.471   1.961  1.00  1.00
ATOM      7  NL  ALA     1      -1.392   0.653   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -2.018   0.061   0.177  1.00  1.00
ATOM      9  CA  ALA     1      -0.005   0.219   0.569  1.00  1.00
ATOM     10  HA  ALA     1       0.083  -0.615   1.230  1.00  1.00
ATOM     11  CB  ALA     1       0.266  -0.275  -0.863  1.00  1.00
ATOM     15  CRP ALA     1       1.126   1.166   0.993  1.00  1.00
ATOM     16  OR  ALA     1       1.918   0.834   1.868  1.00  1.00
ATOM     17  NR  ALA     1       1.248   2.346   0.359  1.00  1.00
ATOM     18  HR  ALA     1       0.548   2.609  -0.299  1.00  1.00
ATOM     19  CR  ALA     1       2.271   3.308   0.675  1.00  1.00
END
REMARK X=28 Y=29 
ATOM      1  CL  ALA     1      -3.438   1.702   1.306  1.00  1.00
ATOM      5  CLP ALA     1      -1.962   1.659   1.317  1.00  1.00
ATOM      6  OL  ALA     1      -1.332   2.532   1.870  1.00  1.00
ATOM      7  NL  ALA     1      -1.406   0.632   0.671  1.00  1.00
ATOM      8  HL  ALA     1      -2.029   0.002   0.252  1.00  1.00
ATOM      9  CA  ALA     1      -0.007   0.228   0.554  1.00  1.00
ATOM     10  HA  ALA     1       0.103  -0.631   1.184  1.00  1.00
ATOM     11  CB  ALA     1       0.255  -0.224  -0.899  1.00  1.00
ATOM     15  CRP ALA     1       1.124   1.169   1.002  1.00  1.00
ATOM     16  OR  ALA     1       1.889   0.829   1.901  1.00  1.00
ATOM     17  NR  ALA     1       1.265   2.342   0.365  1.00  1.00
ATOM     18  HR  ALA     1       0.590   2.614  -0.306  1.00  1.00
ATOM     19  CR  ALA     1       2.313   3.280   0.698  1.00  1.00
END
REMARK X=29 Y=30 
ATOM      1  CL  ALA     1      -3.441   1.677   1.342  1.00  1.00
ATOM      5  CLP ALA     1      -1.971   1.666   1.304  1.00  1.00
ATOM      6  OL  ALA     1      -1.348   2.594   1.774  1.00  1.00
ATOM      7  NL  ALA     1      -1.408   0.602   0.696  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.062   0.329  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.235   0.538  1.00  1.00
ATOM     10  HA  ALA     1       0.114  -0.660   1.127  1.00  1.00
ATOM     11  CB  ALA     1       0.223  -0.161  -0.935  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.153   1.020  1.00  1.00
ATOM     16  OR  ALA     1       1.857   0.813   1.931  1.00  1.00
ATOM     17  NR  ALA     1       1.290   2.335   0.385  1.00  1.00
ATOM     18  HR  ALA     1       0.632   2.617  -0.298  1.00  1.00
ATOM     19  CR  ALA     1       2.337   3.252   0.749  1.00  1.00
END
REMARK X=30 Y=31 
ATOM      1  CL  ALA     1      -3.443   1.670   1.352  1.00  1.00
ATOM      5  CLP ALA     1      -1.973   1.670   1.295  1.00  1.00
ATOM      6  OL  ALA     1      -1.351   2.609   1.744  1.00  1.00
ATOM      7  NL  ALA     1      -1.409   0.597   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.076   0.355  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.237   0.533  1.00  1.00
ATOM     10  HA  ALA     1       0.119  -0.663   1.113  1.00  1.00
ATOM     11  CB  ALA     1       0.217  -0.147  -0.945  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.152   1.023  1.00  1.00
ATOM     16  OR  ALA     1       1.849   0.808   1.938  1.00  1.00
ATOM     17  NR  ALA     1       1.296   2.334   0.388  1.00  1.00
ATOM     18  HR  ALA     1       0.638   2.620  -0.293  1.00  1.00
ATOM     19  CR  ALA     1       2.342   3.249   0.754  1.00  1.00
END
REMARK X=31 Y=32 
ATOM      1  CL  ALA     1      -3.451   1.630   1.422  1.00  1.00
ATOM      5  CLP ALA     1      -1.983   1.689   1.248  1.00  1.00
ATOM      6  OL  ALA     1      -1.374   2.689   1.550  1.00  1.00
ATOM      7  NL  ALA     1      -1.421   0.569   0.756  1.00  1.00
ATOM      8  HL  ALA     1      -2.045  -0.151   0.513  1.00  1.00
ATOM      9  CA  ALA     1      -0.017   0.248   0.499  1.00  1.00
ATOM     10  HA  ALA     1       0.149  -0.681   1.023  1.00  1.00
ATOM     11  CB  ALA     1       0.171  -0.057  -0.999  1.00  1.00
ATOM     15  CRP ALA     1       1.111   1.147   1.033  1.00  1.00
ATOM     16  OR  ALA     1       1.807   0.781   1.969  1.00  1.00
ATOM     17  NR  ALA     1       1.327   2.329   0.410  1.00  1.00
ATOM     18  HR  ALA     1       0.679   2.635  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.372   3.237   0.799  1.00  1.00
END
REMARK X=32 Y=33 
ATOM      1  CL  ALA     1      -3.331   1.449   1.617  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.399   1.408  1.00  1.00
ATOM      6  OL  ALA     1      -1.169   2.255   1.904  1.00  1.00
ATOM      7  NL  ALA     1      -1.424   0.371   0.676  1.00  1.00
ATOM      8  HL  ALA     1      -2.118  -0.203   0.289  1.00  1.00
ATOM      9  CA  ALA     1      -0.062   0.001   0.310  1.00  1.00
ATOM     10  HA  ALA     1      -0.008  -1.054   0.497  1.00  1.00
ATOM     11  CB  ALA     1       0.131   0.162  -1.216  1.00  1.00
ATOM     15  CRP ALA     1       1.142   0.546   1.099  1.00  1.00
ATOM     16  OR  ALA     1       1.741  -0.171   1.894  1.00  1.00
ATOM     17  NR  ALA     1       1.537   1.815   0.864  1.00  1.00
ATOM     18  HR  ALA     1       0.963   2.391   0.297  1.00  1.00
ATOM     19  CR  ALA     1       2.669   2.426   1.513  1.00  1.00
END
REMARK X=33 Y=34 
ATOM      1  CL  ALA     1      -3.321   1.436   1.650  1.00  1.00
ATOM      5  CLP ALA     1      -1.870   1.422   1.372  1.00  1.00
ATOM      6  OL  ALA     1      -1.182   2.323   1.789  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.347   0.697  1.00  1.00
ATOM      8  HL  ALA     1      -2.106  -0.263   0.374  1.00  1.00
ATOM      9  CA  ALA     1      -0.057   0.008   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.002  -1.051   0.446  1.00  1.00
ATOM     11  CB  ALA     1       0.113   0.213  -1.212  1.00  1.00
ATOM     15  CRP ALA     1       1.139   0.538   1.102  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.196   1.881  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.803   0.879  1.00  1.00
ATOM     18  HR  ALA     1       0.972   2.397   0.326  1.00  1.00
ATOM     19  CR  ALA     1       2.672   2.407   1.539  1.00  1.00
END
REMARK X=34 Y=35 
ATOM      1  CL  ALA     1      -3.318   1.434   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -1.871   1.426   1.363  1.00  1.00
ATOM      6  OL  ALA     1      -1.186   2.341   1.756  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.343   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.101  -0.279   0.398  1.00  1.00
ATOM      9  CA  ALA     1      -0.058   0.010   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.005  -1.051   0.433  1.00  1.00
ATOM     11  CB  ALA     1       0.109   0.227  -1.215  1.00  1.00
ATOM     15  CRP ALA     1       1.138   0.536   1.100  1.00  1.00
ATOM     16  OR  ALA     1       1.723  -0.202   1.878  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.802   0.887  1.00  1.00
ATOM     18  HR  ALA     1       0.970   2.398   0.335  1.00  1.00
ATOM     19  CR  ALA     1       2.675   2.402   1.547  1.00  1.00
END
REMARK X=35 Y=36 
ATOM      1  CL  ALA     1      -3.297   1.417   1.700  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.437   1.310  1.00  1.00
ATOM      6  OL  ALA     1      -1.214   2.432   1.560  1.00  1.00
ATOM      7  NL  ALA     1      -1.412   0.320   0.746  1.00  1.00
ATOM      8  HL  ALA     1      -2.060  -0.372   0.544  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.025   0.282  1.00  1.00
ATOM     10  HA  ALA     1       0.023  -1.051   0.357  1.00  1.00
ATOM     11  CB  ALA     1       0.071   0.308  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.141   0.510   1.103  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.245   1.863  1.00  1.00
ATOM     17  NR  ALA     1       1.541   1.794   0.938  1.00  1.00
ATOM     18  HR  ALA     1       0.957   2.397   0.401  1.00  1.00
ATOM     19  CR  ALA     1       2.683   2.371   1.604  1.00  1.00
END
REMARK X=36 Y=37 
ATOM      1  CL  ALA     1      -3.283   1.421   1.730  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.449   1.277  1.00  1.00
ATOM      6  OL  ALA     1      -1.222   2.476   1.436  1.00  1.00
ATOM      7  NL  ALA     1      -1.405   0.299   0.773  1.00  1.00
ATOM      8  HL  ALA     1      -2.034  -0.422   0.640  1.00  1.00
ATOM      9  CA  ALA     1      -0.063   0.028   0.272  1.00  1.00
ATOM     10  HA  ALA     1       0.015  -1.050   0.307  1.00  1.00
ATOM     11  CB  ALA     1       0.057   0.364  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.134   0.492   1.093  1.00  1.00
ATOM     16  OR  ALA     1       1.729  -0.288   1.825  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.779   0.976  1.00  1.00
ATOM     18  HR  ALA     1       0.945   2.388   0.456  1.00  1.00
ATOM     19  CR  ALA     1       2.682   2.335   1.653  1.00  1.00
END
REMARK X=37 Y=38 
ATOM      1  CL  ALA     1      -3.265   1.435   1.760  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.457   1.257  1.00  1.00
ATOM      6  OL  ALA     1      -1.229   2.500   1.343  1.00  1.00
ATOM      7  NL  ALA     1      -1.398   0.292   0.802  1.00  1.00
ATOM      8  HL  ALA     1      -2.014  -0.454   0.728  1.00  1.00
ATOM      9  CA  ALA     1      -0.067   0.024   0.264  1.00  1.00
ATOM     10  HA  ALA     1       0.011  -1.049   0.257  1.00  1.00
ATOM     11  CB  ALA     1       0.028   0.426  -1.206  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.464   1.092  1.00  1.00
ATOM     16  OR  ALA     1       1.748  -0.346   1.781  1.00  1.00
ATOM     17  NR  ALA     1       1.532   1.754   1.029  1.00  1.00
ATOM     18  HR  ALA     1       0.931   2.385   0.536  1.00  1.00
ATOM     19  CR  ALA     1       2.676   2.280   1.721  1.00  1.00
END
REMARK X=38 Y=39 
ATOM      1  CL  ALA     1      -3.236   1.453   1.772  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.473   1.217  1.00  1.00
ATOM      6  OL  ALA     1      -1.244   2.522   1.222  1.00  1.00
ATOM      7  NL  ALA     1      -1.388   0.292   0.824  1.00  1.00
ATOM      8  HL  ALA     1      -1.982  -0.485   0.827  1.00  1.00
ATOM      9  CA  ALA     1      -0.066   0.031   0.248  1.00  1.00
ATOM     10  HA  ALA     1       0.018  -1.048   0.230  1.00  1.00
ATOM     11  CB  ALA     1       0.011   0.464  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.452   1.088  1.00  1.00
ATOM     16  OR  ALA     1       1.767  -0.373   1.737  1.00  1.00
ATOM     17  NR  ALA     1       1.517   1.749   1.061  1.00  1.00
ATOM     18  HR  ALA     1       0.906   2.387   0.586  1.00  1.00
ATOM     19  CR  ALA     1       2.660   2.262   1.754  1.00  1.00
END
REMARK X=39 Y=40 
ATOM      1  CL  ALA     1      -3.225   1.461   1.784  1.00  1.00
ATOM      5  CLP ALA     1      -1.878   1.466   1.191  1.00  1.00
ATOM      6  OL  ALA     1      -1.276   2.527   1.106  1.00  1.00
ATOM      7  NL  ALA     1      -1.375   0.274   0.839  1.00  1.00
ATOM      8  HL  ALA     1      -1.947  -0.517   0.921  1.00  1.00
ATOM      9  CA  ALA     1      -0.077   0.024   0.236  1.00  1.00
ATOM     10  HA  ALA     1       0.009  -1.048   0.194  1.00  1.00
ATOM     11  CB  ALA     1      -0.004   0.503  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.436   1.066  1.00  1.00
ATOM     16  OR  ALA     1       1.800  -0.403   1.678  1.00  1.00
ATOM     17  NR  ALA     1       1.483   1.736   1.091  1.00  1.00
ATOM     18  HR  ALA     1       0.861   2.388   0.647  1.00  1.00
ATOM     19  CR  ALA     1       2.642   2.246   1.792  1.00  1.00
END
REMARK X=40 Y=41 
ATOM      1  CL  ALA     1      -3.212   1.465   1.797  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.470   1.168  1.00  1.00
ATOM      6  OL  ALA     1      -1.286   2.526   1.008  1.00  1.00
ATOM      7  NL  ALA     1      -1.363   0.265   0.860  1.00  1.00
ATOM      8  HL  ALA     1      -1.914  -0.534   1.016  1.00  1.00
ATOM      9  CA  ALA     1      -0.074   0.012   0.232  1.00  1.00
ATOM     10  HA  ALA     1       0.001  -1.058   0.173  1.00  1.00
ATOM     11  CB  ALA     1      -0.020   0.528  -1.210  1.00  1.00
ATOM     15  CRP ALA     1       1.147   0.408   1.060  1.00  1.00
ATOM     16  OR  ALA     1       1.827  -0.445   1.625  1.00  1.00
ATOM     17  NR  ALA     1       1.461   1.721   1.140  1.00  1.00
ATOM     18  HR  ALA     1       0.821   2.361   0.731  1.00  1.00
ATOM     19  CR  ALA     1       2.614   2.214   1.845  1.00  1.00
END
REMARK X=41 Y=42 
ATOM      1  CL  ALA     1      -3.185   1.487   1.790  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.480   1.139  1.00  1.00
ATOM      6  OL  ALA     1      -1.293   2.532   0.896  1.00  1.00
ATOM      7  NL  ALA     1      -1.349   0.268   0.862  1.00  1.00
ATOM      8  HL  ALA     1      -1.881  -0.527   1.095  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.013   0.226  1.00  1.00
ATOM     10  HA  ALA     1      -0.006  -1.063   0.151  1.00  1.00
ATOM     11  CB  ALA     1      -0.019   0.539  -1.224  1.00  1.00
ATOM     15  CRP ALA     1       1.170   0.398   1.031  1.00  1.00
ATOM     16  OR  ALA     1       1.871  -0.463   1.540  1.00  1.00
ATOM     17  NR  ALA     1       1.447   1.706   1.159  1.00  1.00
ATOM     18  HR  ALA     1       0.788   2.362   0.800  1.00  1.00
ATOM     19  CR  ALA     1       2.602   2.205   1.868  1.00  1.00
END
REMARK X=42 Y=43 
ATOM      1  CL  ALA     1      -3.257   1.605   1.105  1.00  1.00
ATOM      5  CLP ALA     1      -1.941   1.459   0.447  1.00  1.00
ATOM      6  OL  ALA     1      -1.481   2.369  -0.223  1.00  1.00
ATOM      7  NL  ALA     1      -1.303   0.291   0.647  1.00  1.00
ATOM      8  HL  ALA     1      -1.743  -0.379   1.229  1.00  1.00
ATOM      9  CA  ALA     1      -0.011  -0.077   0.099  1.00  1.00
ATOM     10  HA  ALA     1       0.155  -1.099   0.417  1.00  1.00
ATOM     11  CB  ALA     1       0.001  -0.097  -1.439  1.00  1.00
ATOM     15  CRP ALA     1       1.191   0.673   0.683  1.00  1.00
ATOM     16  OR  ALA     1       2.015   0.103   1.375  1.00  1.00
ATOM     17  NR  ALA     1       1.303   1.983   0.393  1.00  1.00
ATOM     18  HR  ALA     1       0.553   2.411  -0.109  1.00  1.00
ATOM     19  CR  ALA     1       2.395   2.811   0.843  1.00  1.00
END
FIXED
  
  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
# PLUMED interprets the command:
# rmsd: RMSD SQUARED TYPE=OPTIMAL REFERENCE=regtest/trajectories/path_msd/allv.pdb
# as follows (Click the red comment above to revert to the short version of the input):
rmsd_refThe CONSTANT action with label rmsd_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd_ref
matrix
the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=
regtest/trajectories/path_msd/allv.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/trajectories/path_msd/allv.pdb
    
REMARK X=1 Y=2 
ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00
ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00
ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00
ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00
ATOM      8  HL  ALA     1      -1.845   0.961  -0.011  1.00  1.00
ATOM      9  CA  ALA     1      -0.003  -0.019   0.021  1.00  1.00
ATOM     10  HA  ALA     1       0.205  -1.051   0.259  1.00  1.00
ATOM     11  CB  ALA     1       0.009   0.135  -1.509  1.00  1.00
ATOM     15  CRP ALA     1       1.121   0.799   0.663  1.00  1.00
ATOM     16  OR  ALA     1       1.723   1.669   0.043  1.00  1.00
ATOM     17  NR  ALA     1       1.423   0.519   1.941  1.00  1.00
ATOM     18  HR  ALA     1       0.873  -0.161   2.413  1.00  1.00
ATOM     19  CR  ALA     1       2.477   1.187   2.675  1.00  1.00
END
FIXED
REMARK X=2 Y=3 
ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00
ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00
ATOM      6  OL  ALA     1      -1.201  -0.849   2.425  1.00  1.00
ATOM      7  NL  ALA     1      -1.296   0.337   0.534  1.00  1.00
ATOM      8  HL  ALA     1      -1.807   0.951  -0.044  1.00  1.00
ATOM      9  CA  ALA     1       0.009  -0.067   0.033  1.00  1.00
ATOM     10  HA  ALA     1       0.175  -1.105   0.283  1.00  1.00
ATOM     11  CB  ALA     1       0.027   0.046  -1.501  1.00  1.00
ATOM     15  CRP ALA     1       1.149   0.725   0.654  1.00  1.00
ATOM     16  OR  ALA     1       1.835   1.491  -0.011  1.00  1.00
ATOM     17  NR  ALA     1       1.380   0.537   1.968  1.00  1.00
ATOM     18  HR  ALA     1       0.764  -0.060   2.461  1.00  1.00
ATOM     19  CR  ALA     1       2.431   1.195   2.683  1.00  1.00
END
REMARK X=3 Y=4 
ATOM      1  CL  ALA     1      -2.990   0.383   2.277  1.00  1.00
ATOM      5  CLP ALA     1      -1.664  -0.085   1.831  1.00  1.00
ATOM      6  OL  ALA     1      -0.987  -0.835   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.227   0.364   0.646  1.00  1.00
ATOM      8  HL  ALA     1      -1.798   0.982   0.124  1.00  1.00
ATOM      9  CA  ALA     1       0.026  -0.028   0.044  1.00  1.00
ATOM     10  HA  ALA     1       0.224  -1.060   0.284  1.00  1.00
ATOM     11  CB  ALA     1      -0.076   0.107  -1.483  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.776   0.577  1.00  1.00
ATOM     16  OR  ALA     1       1.900   1.463  -0.158  1.00  1.00
ATOM     17  NR  ALA     1       1.494   0.666   1.888  1.00  1.00
ATOM     18  HR  ALA     1       0.882   0.122   2.437  1.00  1.00
ATOM     19  CR  ALA     1       2.580   1.341   2.529  1.00  1.00
END
REMARK X=4 Y=5 
ATOM      1  CL  ALA     1      -3.006   0.350   2.252  1.00  1.00
ATOM      5  CLP ALA     1      -1.680  -0.112   1.826  1.00  1.00
ATOM      6  OL  ALA     1      -1.025  -0.896   2.508  1.00  1.00
ATOM      7  NL  ALA     1      -1.220   0.368   0.654  1.00  1.00
ATOM      8  HL  ALA     1      -1.771   1.013   0.137  1.00  1.00
ATOM      9  CA  ALA     1       0.040  -0.029   0.062  1.00  1.00
ATOM     10  HA  ALA     1       0.210  -1.076   0.277  1.00  1.00
ATOM     11  CB  ALA     1      -0.066   0.148  -1.465  1.00  1.00
ATOM     15  CRP ALA     1       1.241   0.738   0.605  1.00  1.00
ATOM     16  OR  ALA     1       1.986   1.347  -0.125  1.00  1.00
ATOM     17  NR  ALA     1       1.446   0.694   1.940  1.00  1.00
ATOM     18  HR  ALA     1       0.796   0.210   2.481  1.00  1.00
ATOM     19  CR  ALA     1       2.544   1.350   2.582  1.00  1.00
END
REMARK X=5 Y=6 
ATOM      1  CL  ALA     1      -3.002   0.343   2.271  1.00  1.00
ATOM      5  CLP ALA     1      -1.672  -0.125   1.828  1.00  1.00
ATOM      6  OL  ALA     1      -1.028  -0.942   2.486  1.00  1.00
ATOM      7  NL  ALA     1      -1.213   0.373   0.670  1.00  1.00
ATOM      8  HL  ALA     1      -1.752   1.033   0.169  1.00  1.00
ATOM      9  CA  ALA     1       0.041  -0.032   0.055  1.00  1.00
ATOM     10  HA  ALA     1       0.201  -1.079   0.245  1.00  1.00
ATOM     11  CB  ALA     1      -0.079   0.194  -1.466  1.00  1.00
ATOM     15  CRP ALA     1       1.257   0.720   0.601  1.00  1.00
ATOM     16  OR  ALA     1       2.057   1.240  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.422   0.730   1.942  1.00  1.00
ATOM     18  HR  ALA     1       0.740   0.303   2.500  1.00  1.00
ATOM     19  CR  ALA     1       2.528   1.373   2.598  1.00  1.00
END
REMARK X=6 Y=7 
ATOM      1  CL  ALA     1      -3.144   1.457   1.417  1.00  1.00
ATOM      5  CLP ALA     1      -1.943   0.587   1.450  1.00  1.00
ATOM      6  OL  ALA     1      -1.588   0.028   2.480  1.00  1.00
ATOM      7  NL  ALA     1      -1.281   0.449   0.306  1.00  1.00
ATOM      8  HL  ALA     1      -1.578   0.914  -0.520  1.00  1.00
ATOM      9  CA  ALA     1      -0.132  -0.428   0.139  1.00  1.00
ATOM     10  HA  ALA     1      -0.264  -1.291   0.758  1.00  1.00
ATOM     11  CB  ALA     1      -0.066  -0.855  -1.329  1.00  1.00
ATOM     15  CRP ALA     1       1.193   0.220   0.554  1.00  1.00
ATOM     16  OR  ALA     1       2.195   0.098  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.224   0.872   1.737  1.00  1.00
ATOM     18  HR  ALA     1       0.399   0.943   2.273  1.00  1.00
ATOM     19  CR  ALA     1       2.413   1.511   2.254  1.00  1.00
END
REMARK X=7 Y=8 
ATOM      1  CL  ALA     1      -3.140   1.441   1.453  1.00  1.00
ATOM      5  CLP ALA     1      -1.944   0.576   1.465  1.00  1.00
ATOM      6  OL  ALA     1      -1.587  -0.018   2.487  1.00  1.00
ATOM      7  NL  ALA     1      -1.274   0.465   0.322  1.00  1.00
ATOM      8  HL  ALA     1      -1.571   0.957  -0.486  1.00  1.00
ATOM      9  CA  ALA     1      -0.124  -0.418   0.135  1.00  1.00
ATOM     10  HA  ALA     1      -0.274  -1.304   0.729  1.00  1.00
ATOM     11  CB  ALA     1      -0.063  -0.813  -1.347  1.00  1.00
ATOM     15  CRP ALA     1       1.201   0.199   0.572  1.00  1.00
ATOM     16  OR  ALA     1       2.227   0.007  -0.072  1.00  1.00
ATOM     17  NR  ALA     1       1.215   0.910   1.709  1.00  1.00
ATOM     18  HR  ALA     1       0.369   1.020   2.200  1.00  1.00
ATOM     19  CR  ALA     1       2.393   1.536   2.237  1.00  1.00
END
REMARK X=8 Y=9 
ATOM      1  CL  ALA     1      -3.140   1.420   1.442  1.00  1.00
ATOM      5  CLP ALA     1      -1.948   0.546   1.448  1.00  1.00
ATOM      6  OL  ALA     1      -1.618  -0.065   2.460  1.00  1.00
ATOM      7  NL  ALA     1      -1.255   0.469   0.311  1.00  1.00
ATOM      8  HL  ALA     1      -1.538   0.979  -0.490  1.00  1.00
ATOM      9  CA  ALA     1      -0.107  -0.412   0.124  1.00  1.00
ATOM     10  HA  ALA     1      -0.257  -1.312   0.685  1.00  1.00
ATOM     11  CB  ALA     1      -0.028  -0.770  -1.375  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.186   0.600  1.00  1.00
ATOM     16  OR  ALA     1       2.269  -0.069   0.026  1.00  1.00
ATOM     17  NR  ALA     1       1.193   0.966   1.687  1.00  1.00
ATOM     18  HR  ALA     1       0.333   1.114   2.120  1.00  1.00
ATOM     19  CR  ALA     1       2.377   1.589   2.240  1.00  1.00
END
REMARK X=9 Y=10 
ATOM      1  CL  ALA     1      -3.110   1.698   0.880  1.00  1.00
ATOM      5  CLP ALA     1      -2.021   0.734   1.142  1.00  1.00
ATOM      6  OL  ALA     1      -1.859   0.257   2.258  1.00  1.00
ATOM      7  NL  ALA     1      -1.229   0.414   0.114  1.00  1.00
ATOM      8  HL  ALA     1      -1.371   0.826  -0.771  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.593   0.188  1.00  1.00
ATOM     10  HA  ALA     1      -0.481  -1.374   0.851  1.00  1.00
ATOM     11  CB  ALA     1       0.011  -1.180  -1.220  1.00  1.00
ATOM     15  CRP ALA     1       1.163  -0.060   0.716  1.00  1.00
ATOM     16  OR  ALA     1       2.227  -0.564   0.393  1.00  1.00
ATOM     17  NR  ALA     1       1.127   0.960   1.594  1.00  1.00
ATOM     18  HR  ALA     1       0.234   1.295   1.847  1.00  1.00
ATOM     19  CR  ALA     1       2.303   1.549   2.172  1.00  1.00
END
REMARK X=10 Y=11 
ATOM      1  CL  ALA     1      -3.139   1.652   0.924  1.00  1.00
ATOM      5  CLP ALA     1      -2.039   0.698   1.169  1.00  1.00
ATOM      6  OL  ALA     1      -1.868   0.201   2.278  1.00  1.00
ATOM      7  NL  ALA     1      -1.239   0.411   0.139  1.00  1.00
ATOM      8  HL  ALA     1      -1.385   0.842  -0.737  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.574   0.193  1.00  1.00
ATOM     10  HA  ALA     1      -0.477  -1.381   0.833  1.00  1.00
ATOM     11  CB  ALA     1       0.029  -1.142  -1.231  1.00  1.00
ATOM     15  CRP ALA     1       1.162  -0.048   0.731  1.00  1.00
ATOM     16  OR  ALA     1       2.220  -0.597   0.472  1.00  1.00
ATOM     17  NR  ALA     1       1.122   1.024   1.537  1.00  1.00
ATOM     18  HR  ALA     1       0.233   1.395   1.752  1.00  1.00
ATOM     19  CR  ALA     1       2.300   1.629   2.102  1.00  1.00
END
REMARK X=11 Y=12 
ATOM      1  CL  ALA     1      -3.706   1.088   0.468  1.00  1.00
ATOM      5  CLP ALA     1      -2.458   0.598   1.082  1.00  1.00
ATOM      6  OL  ALA     1      -2.390   0.404   2.277  1.00  1.00
ATOM      7  NL  ALA     1      -1.427   0.382   0.258  1.00  1.00
ATOM      8  HL  ALA     1      -1.513   0.559  -0.713  1.00  1.00
ATOM      9  CA  ALA     1      -0.157  -0.192   0.685  1.00  1.00
ATOM     10  HA  ALA     1      -0.343  -0.912   1.470  1.00  1.00
ATOM     11  CB  ALA     1       0.462  -0.936  -0.512  1.00  1.00
ATOM     15  CRP ALA     1       0.840   0.814   1.241  1.00  1.00
ATOM     16  OR  ALA     1       2.034   0.549   1.354  1.00  1.00
ATOM     17  NR  ALA     1       0.368   2.017   1.650  1.00  1.00
ATOM     18  HR  ALA     1      -0.613   2.169   1.589  1.00  1.00
ATOM     19  CR  ALA     1       1.215   3.044   2.195  1.00  1.00
END
REMARK X=12 Y=13 
ATOM      1  CL  ALA     1      -3.699   1.173   0.487  1.00  1.00
ATOM      5  CLP ALA     1      -2.464   0.631   1.079  1.00  1.00
ATOM      6  OL  ALA     1      -2.402   0.386   2.275  1.00  1.00
ATOM      7  NL  ALA     1      -1.434   0.437   0.260  1.00  1.00
ATOM      8  HL  ALA     1      -1.516   0.652  -0.701  1.00  1.00
ATOM      9  CA  ALA     1      -0.174  -0.174   0.667  1.00  1.00
ATOM     10  HA  ALA     1      -0.377  -0.924   1.411  1.00  1.00
ATOM     11  CB  ALA     1       0.451  -0.859  -0.570  1.00  1.00
ATOM     15  CRP ALA     1       0.839   0.801   1.280  1.00  1.00
ATOM     16  OR  ALA     1       1.999   0.474   1.468  1.00  1.00
ATOM     17  NR  ALA     1       0.404   2.024   1.627  1.00  1.00
ATOM     18  HR  ALA     1      -0.565   2.225   1.505  1.00  1.00
ATOM     19  CR  ALA     1       1.262   3.025   2.214  1.00  1.00
END
REMARK X=13 Y=14 
ATOM      1  CL  ALA     1      -3.653   0.990   1.121  1.00  1.00
ATOM      5  CLP ALA     1      -2.321   0.364   1.249  1.00  1.00
ATOM      6  OL  ALA     1      -2.006  -0.222   2.265  1.00  1.00
ATOM      7  NL  ALA     1      -1.498   0.501   0.205  1.00  1.00
ATOM      8  HL  ALA     1      -1.794   0.978  -0.603  1.00  1.00
ATOM      9  CA  ALA     1      -0.190  -0.127   0.128  1.00  1.00
ATOM     10  HA  ALA     1      -0.216  -1.086   0.627  1.00  1.00
ATOM     11  CB  ALA     1       0.159  -0.359  -1.359  1.00  1.00
ATOM     15  CRP ALA     1       0.933   0.668   0.793  1.00  1.00
ATOM     16  OR  ALA     1       2.107   0.313   0.705  1.00  1.00
ATOM     17  NR  ALA     1       0.604   1.770   1.498  1.00  1.00
ATOM     18  HR  ALA     1      -0.359   1.986   1.593  1.00  1.00
ATOM     19  CR  ALA     1       1.573   2.595   2.158  1.00  1.00
END
REMARK X=14 Y=15 
ATOM      1  CL  ALA     1      -3.641   0.954   1.179  1.00  1.00
ATOM      5  CLP ALA     1      -2.294   0.335   1.290  1.00  1.00
ATOM      6  OL  ALA     1      -1.964  -0.273   2.288  1.00  1.00
ATOM      7  NL  ALA     1      -1.485   0.499   0.235  1.00  1.00
ATOM      8  HL  ALA     1      -1.803   0.995  -0.564  1.00  1.00
ATOM      9  CA  ALA     1      -0.175  -0.118   0.130  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.077   0.601  1.00  1.00
ATOM     11  CB  ALA     1       0.162  -0.300  -1.355  1.00  1.00
ATOM     15  CRP ALA     1       0.952   0.671   0.815  1.00  1.00
ATOM     16  OR  ALA     1       2.104   0.260   0.791  1.00  1.00
ATOM     17  NR  ALA     1       0.633   1.808   1.450  1.00  1.00
ATOM     18  HR  ALA     1      -0.328   2.065   1.503  1.00  1.00
ATOM     19  CR  ALA     1       1.608   2.627   2.129  1.00  1.00
END
REMARK X=15 Y=16 
ATOM      1  CL  ALA     1      -3.635   0.925   1.244  1.00  1.00
ATOM      5  CLP ALA     1      -2.297   0.305   1.309  1.00  1.00
ATOM      6  OL  ALA     1      -1.941  -0.334   2.290  1.00  1.00
ATOM      7  NL  ALA     1      -1.500   0.490   0.251  1.00  1.00
ATOM      8  HL  ALA     1      -1.827   1.009  -0.537  1.00  1.00
ATOM      9  CA  ALA     1      -0.178  -0.110   0.119  1.00  1.00
ATOM     10  HA  ALA     1      -0.205  -1.094   0.536  1.00  1.00
ATOM     11  CB  ALA     1       0.147  -0.217  -1.379  1.00  1.00
ATOM     15  CRP ALA     1       0.943   0.643   0.832  1.00  1.00
ATOM     16  OR  ALA     1       2.074   0.198   0.871  1.00  1.00
ATOM     17  NR  ALA     1       0.637   1.821   1.423  1.00  1.00
ATOM     18  HR  ALA     1      -0.311   2.123   1.418  1.00  1.00
ATOM     19  CR  ALA     1       1.602   2.629   2.109  1.00  1.00
END
REMARK X=16 Y=17 
ATOM      1  CL  ALA     1      -3.632   0.856   1.331  1.00  1.00
ATOM      5  CLP ALA     1      -2.282   0.250   1.355  1.00  1.00
ATOM      6  OL  ALA     1      -1.906  -0.403   2.301  1.00  1.00
ATOM      7  NL  ALA     1      -1.515   0.478   0.275  1.00  1.00
ATOM      8  HL  ALA     1      -1.860   0.990  -0.485  1.00  1.00
ATOM      9  CA  ALA     1      -0.192  -0.105   0.098  1.00  1.00
ATOM     10  HA  ALA     1      -0.204  -1.121   0.473  1.00  1.00
ATOM     11  CB  ALA     1       0.129  -0.136  -1.408  1.00  1.00
ATOM     15  CRP ALA     1       0.931   0.615   0.844  1.00  1.00
ATOM     16  OR  ALA     1       2.043   0.122   0.934  1.00  1.00
ATOM     17  NR  ALA     1       0.651   1.819   1.388  1.00  1.00
ATOM     18  HR  ALA     1      -0.283   2.155   1.349  1.00  1.00
ATOM     19  CR  ALA     1       1.624   2.595   2.115  1.00  1.00
END
REMARK X=17 Y=18 
ATOM      1  CL  ALA     1      -3.628   0.823   1.358  1.00  1.00
ATOM      5  CLP ALA     1      -2.277   0.241   1.370  1.00  1.00
ATOM      6  OL  ALA     1      -1.871  -0.396   2.325  1.00  1.00
ATOM      7  NL  ALA     1      -1.525   0.469   0.284  1.00  1.00
ATOM      8  HL  ALA     1      -1.898   0.970  -0.482  1.00  1.00
ATOM      9  CA  ALA     1      -0.195  -0.094   0.086  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.122   0.423  1.00  1.00
ATOM     11  CB  ALA     1       0.146  -0.058  -1.413  1.00  1.00
ATOM     15  CRP ALA     1       0.919   0.599   0.874  1.00  1.00
ATOM     16  OR  ALA     1       1.997   0.065   1.039  1.00  1.00
ATOM     17  NR  ALA     1       0.655   1.830   1.373  1.00  1.00
ATOM     18  HR  ALA     1      -0.248   2.200   1.261  1.00  1.00
ATOM     19  CR  ALA     1       1.625   2.581   2.124  1.00  1.00
END
REMARK X=18 Y=19 
ATOM      1  CL  ALA     1      -3.539   0.055   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -2.117  -0.208   1.378  1.00  1.00
ATOM      6  OL  ALA     1      -1.453  -0.902   2.125  1.00  1.00
ATOM      7  NL  ALA     1      -1.602   0.351   0.289  1.00  1.00
ATOM      8  HL  ALA     1      -2.185   0.875  -0.310  1.00  1.00
ATOM      9  CA  ALA     1      -0.243   0.129  -0.186  1.00  1.00
ATOM     10  HA  ALA     1      -0.041  -0.924  -0.159  1.00  1.00
ATOM     11  CB  ALA     1      -0.153   0.625  -1.651  1.00  1.00
ATOM     15  CRP ALA     1       0.852   0.806   0.637  1.00  1.00
ATOM     16  OR  ALA     1       2.007   0.400   0.594  1.00  1.00
ATOM     17  NR  ALA     1       0.508   1.855   1.401  1.00  1.00
ATOM     18  HR  ALA     1      -0.445   2.112   1.454  1.00  1.00
ATOM     19  CR  ALA     1       1.460   2.569   2.226  1.00  1.00
END
REMARK X=19 Y=20 
ATOM      1  CL  ALA     1      -3.578   0.084   1.603  1.00  1.00
ATOM      5  CLP ALA     1      -2.140  -0.156   1.375  1.00  1.00
ATOM      6  OL  ALA     1      -1.473  -0.732   2.197  1.00  1.00
ATOM      7  NL  ALA     1      -1.623   0.335   0.237  1.00  1.00
ATOM      8  HL  ALA     1      -2.220   0.753  -0.416  1.00  1.00
ATOM      9  CA  ALA     1      -0.253   0.120  -0.195  1.00  1.00
ATOM     10  HA  ALA     1      -0.048  -0.931  -0.153  1.00  1.00
ATOM     11  CB  ALA     1      -0.128   0.612  -1.663  1.00  1.00
ATOM     15  CRP ALA     1       0.823   0.801   0.637  1.00  1.00
ATOM     16  OR  ALA     1       1.969   0.367   0.665  1.00  1.00
ATOM     17  NR  ALA     1       0.477   1.912   1.333  1.00  1.00
ATOM     18  HR  ALA     1      -0.468   2.199   1.317  1.00  1.00
ATOM     19  CR  ALA     1       1.410   2.627   2.163  1.00  1.00
END
REMARK X=20 Y=21 
ATOM      1  CL  ALA     1      -3.113   1.661   1.504  1.00  1.00
ATOM      5  CLP ALA     1      -1.769   1.059   1.566  1.00  1.00
ATOM      6  OL  ALA     1      -1.201   0.940   2.629  1.00  1.00
ATOM      7  NL  ALA     1      -1.219   0.714   0.392  1.00  1.00
ATOM      8  HL  ALA     1      -1.742   0.797  -0.435  1.00  1.00
ATOM      9  CA  ALA     1       0.058   0.023   0.242  1.00  1.00
ATOM     10  HA  ALA     1      -0.001  -0.896   0.782  1.00  1.00
ATOM     11  CB  ALA     1       0.235  -0.295  -1.249  1.00  1.00
ATOM     15  CRP ALA     1       1.299   0.757   0.745  1.00  1.00
ATOM     16  OR  ALA     1       2.276   0.138   1.135  1.00  1.00
ATOM     17  NR  ALA     1       1.277   2.102   0.736  1.00  1.00
ATOM     18  HR  ALA     1       0.447   2.567   0.458  1.00  1.00
ATOM     19  CR  ALA     1       2.391   2.896   1.191  1.00  1.00
END
REMARK X=21 Y=22 
ATOM      1  CL  ALA     1      -3.089   1.850   1.546  1.00  1.00
ATOM      5  CLP ALA     1      -1.667   1.457   1.629  1.00  1.00
ATOM      6  OL  ALA     1      -0.974   1.868   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.204   0.683   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -1.844   0.360  -0.021  1.00  1.00
ATOM      9  CA  ALA     1       0.126   0.105   0.564  1.00  1.00
ATOM     10  HA  ALA     1       0.239  -0.555   1.391  1.00  1.00
ATOM     11  CB  ALA     1       0.215  -0.722  -0.739  1.00  1.00
ATOM     15  CRP ALA     1       1.311   1.068   0.623  1.00  1.00
ATOM     16  OR  ALA     1       2.369   0.726   1.149  1.00  1.00
ATOM     17  NR  ALA     1       1.156   2.292   0.077  1.00  1.00
ATOM     18  HR  ALA     1       0.273   2.549  -0.285  1.00  1.00
ATOM     19  CR  ALA     1       2.201   3.277   0.107  1.00  1.00
END
REMARK X=22 Y=23 
ATOM      1  CL  ALA     1      -3.102   1.775   1.619  1.00  1.00
ATOM      5  CLP ALA     1      -1.661   1.466   1.659  1.00  1.00
ATOM      6  OL  ALA     1      -0.945   1.961   2.476  1.00  1.00
ATOM      7  NL  ALA     1      -1.205   0.663   0.688  1.00  1.00
ATOM      8  HL  ALA     1      -1.854   0.269   0.091  1.00  1.00
ATOM      9  CA  ALA     1       0.147   0.134   0.561  1.00  1.00
ATOM     10  HA  ALA     1       0.300  -0.545   1.355  1.00  1.00
ATOM     11  CB  ALA     1       0.237  -0.632  -0.776  1.00  1.00
ATOM     15  CRP ALA     1       1.306   1.133   0.628  1.00  1.00
ATOM     16  OR  ALA     1       2.361   0.819   1.176  1.00  1.00
ATOM     17  NR  ALA     1       1.129   2.345   0.068  1.00  1.00
ATOM     18  HR  ALA     1       0.252   2.577  -0.315  1.00  1.00
ATOM     19  CR  ALA     1       2.150   3.364   0.108  1.00  1.00
END
REMARK X=23 Y=24 
ATOM      1  CL  ALA     1      -3.137   1.689   1.564  1.00  1.00
ATOM      5  CLP ALA     1      -1.674   1.466   1.595  1.00  1.00
ATOM      6  OL  ALA     1      -0.991   2.041   2.377  1.00  1.00
ATOM      7  NL  ALA     1      -1.178   0.640   0.664  1.00  1.00
ATOM      8  HL  ALA     1      -1.829   0.190   0.106  1.00  1.00
ATOM      9  CA  ALA     1       0.192   0.170   0.547  1.00  1.00
ATOM     10  HA  ALA     1       0.347  -0.550   1.313  1.00  1.00
ATOM     11  CB  ALA     1       0.333  -0.536  -0.821  1.00  1.00
ATOM     15  CRP ALA     1       1.325   1.194   0.686  1.00  1.00
ATOM     16  OR  ALA     1       2.348   0.906   1.293  1.00  1.00
ATOM     17  NR  ALA     1       1.165   2.398   0.103  1.00  1.00
ATOM     18  HR  ALA     1       0.311   2.617  -0.339  1.00  1.00
ATOM     19  CR  ALA     1       2.173   3.424   0.206  1.00  1.00
END
REMARK X=24 Y=25 
ATOM      1  CL  ALA     1      -3.342   1.726   1.297  1.00  1.00
ATOM      5  CLP ALA     1      -1.882   1.644   1.449  1.00  1.00
ATOM      6  OL  ALA     1      -1.296   2.423   2.124  1.00  1.00
ATOM      7  NL  ALA     1      -1.259   0.684   0.740  1.00  1.00
ATOM      8  HL  ALA     1      -1.839   0.091   0.256  1.00  1.00
ATOM      9  CA  ALA     1       0.138   0.295   0.784  1.00  1.00
ATOM     10  HA  ALA     1       0.267  -0.321   1.638  1.00  1.00
ATOM     11  CB  ALA     1       0.437  -0.541  -0.481  1.00  1.00
ATOM     15  CRP ALA     1       1.207   1.385   0.899  1.00  1.00
ATOM     16  OR  ALA     1       2.160   1.248   1.674  1.00  1.00
ATOM     17  NR  ALA     1       1.092   2.478   0.129  1.00  1.00
ATOM     18  HR  ALA     1       0.291   2.586  -0.440  1.00  1.00
ATOM     19  CR  ALA     1       2.044   3.567   0.190  1.00  1.00
END
REMARK X=25 Y=26 
ATOM      1  CL  ALA     1      -3.361   1.726   1.315  1.00  1.00
ATOM      5  CLP ALA     1      -1.890   1.687   1.423  1.00  1.00
ATOM      6  OL  ALA     1      -1.302   2.522   2.029  1.00  1.00
ATOM      7  NL  ALA     1      -1.285   0.691   0.757  1.00  1.00
ATOM      8  HL  ALA     1      -1.865   0.049   0.326  1.00  1.00
ATOM      9  CA  ALA     1       0.123   0.321   0.749  1.00  1.00
ATOM     10  HA  ALA     1       0.270  -0.331   1.585  1.00  1.00
ATOM     11  CB  ALA     1       0.408  -0.470  -0.534  1.00  1.00
ATOM     15  CRP ALA     1       1.192   1.410   0.900  1.00  1.00
ATOM     16  OR  ALA     1       2.114   1.273   1.701  1.00  1.00
ATOM     17  NR  ALA     1       1.111   2.493   0.112  1.00  1.00
ATOM     18  HR  ALA     1       0.326   2.609  -0.490  1.00  1.00
ATOM     19  CR  ALA     1       2.068   3.578   0.188  1.00  1.00
END
REMARK X=26 Y=27 
ATOM      1  CL  ALA     1      -3.419   1.747   1.251  1.00  1.00
ATOM      5  CLP ALA     1      -1.947   1.630   1.371  1.00  1.00
ATOM      6  OL  ALA     1      -1.331   2.379   2.060  1.00  1.00
ATOM      7  NL  ALA     1      -1.380   0.668   0.616  1.00  1.00
ATOM      8  HL  ALA     1      -1.992   0.115   0.104  1.00  1.00
ATOM      9  CA  ALA     1       0.007   0.227   0.571  1.00  1.00
ATOM     10  HA  ALA     1       0.086  -0.578   1.262  1.00  1.00
ATOM     11  CB  ALA     1       0.288  -0.306  -0.835  1.00  1.00
ATOM     15  CRP ALA     1       1.132   1.190   0.974  1.00  1.00
ATOM     16  OR  ALA     1       1.974   0.858   1.808  1.00  1.00
ATOM     17  NR  ALA     1       1.199   2.390   0.352  1.00  1.00
ATOM     18  HR  ALA     1       0.482   2.643  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.218   3.363   0.657  1.00  1.00
END
REMARK X=27 Y=28 
ATOM      1  CL  ALA     1      -3.430   1.748   1.261  1.00  1.00
ATOM      5  CLP ALA     1      -1.958   1.650   1.340  1.00  1.00
ATOM      6  OL  ALA     1      -1.333   2.471   1.961  1.00  1.00
ATOM      7  NL  ALA     1      -1.392   0.653   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -2.018   0.061   0.177  1.00  1.00
ATOM      9  CA  ALA     1      -0.005   0.219   0.569  1.00  1.00
ATOM     10  HA  ALA     1       0.083  -0.615   1.230  1.00  1.00
ATOM     11  CB  ALA     1       0.266  -0.275  -0.863  1.00  1.00
ATOM     15  CRP ALA     1       1.126   1.166   0.993  1.00  1.00
ATOM     16  OR  ALA     1       1.918   0.834   1.868  1.00  1.00
ATOM     17  NR  ALA     1       1.248   2.346   0.359  1.00  1.00
ATOM     18  HR  ALA     1       0.548   2.609  -0.299  1.00  1.00
ATOM     19  CR  ALA     1       2.271   3.308   0.675  1.00  1.00
END
REMARK X=28 Y=29 
ATOM      1  CL  ALA     1      -3.438   1.702   1.306  1.00  1.00
ATOM      5  CLP ALA     1      -1.962   1.659   1.317  1.00  1.00
ATOM      6  OL  ALA     1      -1.332   2.532   1.870  1.00  1.00
ATOM      7  NL  ALA     1      -1.406   0.632   0.671  1.00  1.00
ATOM      8  HL  ALA     1      -2.029   0.002   0.252  1.00  1.00
ATOM      9  CA  ALA     1      -0.007   0.228   0.554  1.00  1.00
ATOM     10  HA  ALA     1       0.103  -0.631   1.184  1.00  1.00
ATOM     11  CB  ALA     1       0.255  -0.224  -0.899  1.00  1.00
ATOM     15  CRP ALA     1       1.124   1.169   1.002  1.00  1.00
ATOM     16  OR  ALA     1       1.889   0.829   1.901  1.00  1.00
ATOM     17  NR  ALA     1       1.265   2.342   0.365  1.00  1.00
ATOM     18  HR  ALA     1       0.590   2.614  -0.306  1.00  1.00
ATOM     19  CR  ALA     1       2.313   3.280   0.698  1.00  1.00
END
REMARK X=29 Y=30 
ATOM      1  CL  ALA     1      -3.441   1.677   1.342  1.00  1.00
ATOM      5  CLP ALA     1      -1.971   1.666   1.304  1.00  1.00
ATOM      6  OL  ALA     1      -1.348   2.594   1.774  1.00  1.00
ATOM      7  NL  ALA     1      -1.408   0.602   0.696  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.062   0.329  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.235   0.538  1.00  1.00
ATOM     10  HA  ALA     1       0.114  -0.660   1.127  1.00  1.00
ATOM     11  CB  ALA     1       0.223  -0.161  -0.935  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.153   1.020  1.00  1.00
ATOM     16  OR  ALA     1       1.857   0.813   1.931  1.00  1.00
ATOM     17  NR  ALA     1       1.290   2.335   0.385  1.00  1.00
ATOM     18  HR  ALA     1       0.632   2.617  -0.298  1.00  1.00
ATOM     19  CR  ALA     1       2.337   3.252   0.749  1.00  1.00
END
REMARK X=30 Y=31 
ATOM      1  CL  ALA     1      -3.443   1.670   1.352  1.00  1.00
ATOM      5  CLP ALA     1      -1.973   1.670   1.295  1.00  1.00
ATOM      6  OL  ALA     1      -1.351   2.609   1.744  1.00  1.00
ATOM      7  NL  ALA     1      -1.409   0.597   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.076   0.355  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.237   0.533  1.00  1.00
ATOM     10  HA  ALA     1       0.119  -0.663   1.113  1.00  1.00
ATOM     11  CB  ALA     1       0.217  -0.147  -0.945  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.152   1.023  1.00  1.00
ATOM     16  OR  ALA     1       1.849   0.808   1.938  1.00  1.00
ATOM     17  NR  ALA     1       1.296   2.334   0.388  1.00  1.00
ATOM     18  HR  ALA     1       0.638   2.620  -0.293  1.00  1.00
ATOM     19  CR  ALA     1       2.342   3.249   0.754  1.00  1.00
END
REMARK X=31 Y=32 
ATOM      1  CL  ALA     1      -3.451   1.630   1.422  1.00  1.00
ATOM      5  CLP ALA     1      -1.983   1.689   1.248  1.00  1.00
ATOM      6  OL  ALA     1      -1.374   2.689   1.550  1.00  1.00
ATOM      7  NL  ALA     1      -1.421   0.569   0.756  1.00  1.00
ATOM      8  HL  ALA     1      -2.045  -0.151   0.513  1.00  1.00
ATOM      9  CA  ALA     1      -0.017   0.248   0.499  1.00  1.00
ATOM     10  HA  ALA     1       0.149  -0.681   1.023  1.00  1.00
ATOM     11  CB  ALA     1       0.171  -0.057  -0.999  1.00  1.00
ATOM     15  CRP ALA     1       1.111   1.147   1.033  1.00  1.00
ATOM     16  OR  ALA     1       1.807   0.781   1.969  1.00  1.00
ATOM     17  NR  ALA     1       1.327   2.329   0.410  1.00  1.00
ATOM     18  HR  ALA     1       0.679   2.635  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.372   3.237   0.799  1.00  1.00
END
REMARK X=32 Y=33 
ATOM      1  CL  ALA     1      -3.331   1.449   1.617  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.399   1.408  1.00  1.00
ATOM      6  OL  ALA     1      -1.169   2.255   1.904  1.00  1.00
ATOM      7  NL  ALA     1      -1.424   0.371   0.676  1.00  1.00
ATOM      8  HL  ALA     1      -2.118  -0.203   0.289  1.00  1.00
ATOM      9  CA  ALA     1      -0.062   0.001   0.310  1.00  1.00
ATOM     10  HA  ALA     1      -0.008  -1.054   0.497  1.00  1.00
ATOM     11  CB  ALA     1       0.131   0.162  -1.216  1.00  1.00
ATOM     15  CRP ALA     1       1.142   0.546   1.099  1.00  1.00
ATOM     16  OR  ALA     1       1.741  -0.171   1.894  1.00  1.00
ATOM     17  NR  ALA     1       1.537   1.815   0.864  1.00  1.00
ATOM     18  HR  ALA     1       0.963   2.391   0.297  1.00  1.00
ATOM     19  CR  ALA     1       2.669   2.426   1.513  1.00  1.00
END
REMARK X=33 Y=34 
ATOM      1  CL  ALA     1      -3.321   1.436   1.650  1.00  1.00
ATOM      5  CLP ALA     1      -1.870   1.422   1.372  1.00  1.00
ATOM      6  OL  ALA     1      -1.182   2.323   1.789  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.347   0.697  1.00  1.00
ATOM      8  HL  ALA     1      -2.106  -0.263   0.374  1.00  1.00
ATOM      9  CA  ALA     1      -0.057   0.008   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.002  -1.051   0.446  1.00  1.00
ATOM     11  CB  ALA     1       0.113   0.213  -1.212  1.00  1.00
ATOM     15  CRP ALA     1       1.139   0.538   1.102  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.196   1.881  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.803   0.879  1.00  1.00
ATOM     18  HR  ALA     1       0.972   2.397   0.326  1.00  1.00
ATOM     19  CR  ALA     1       2.672   2.407   1.539  1.00  1.00
END
REMARK X=34 Y=35 
ATOM      1  CL  ALA     1      -3.318   1.434   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -1.871   1.426   1.363  1.00  1.00
ATOM      6  OL  ALA     1      -1.186   2.341   1.756  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.343   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.101  -0.279   0.398  1.00  1.00
ATOM      9  CA  ALA     1      -0.058   0.010   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.005  -1.051   0.433  1.00  1.00
ATOM     11  CB  ALA     1       0.109   0.227  -1.215  1.00  1.00
ATOM     15  CRP ALA     1       1.138   0.536   1.100  1.00  1.00
ATOM     16  OR  ALA     1       1.723  -0.202   1.878  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.802   0.887  1.00  1.00
ATOM     18  HR  ALA     1       0.970   2.398   0.335  1.00  1.00
ATOM     19  CR  ALA     1       2.675   2.402   1.547  1.00  1.00
END
REMARK X=35 Y=36 
ATOM      1  CL  ALA     1      -3.297   1.417   1.700  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.437   1.310  1.00  1.00
ATOM      6  OL  ALA     1      -1.214   2.432   1.560  1.00  1.00
ATOM      7  NL  ALA     1      -1.412   0.320   0.746  1.00  1.00
ATOM      8  HL  ALA     1      -2.060  -0.372   0.544  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.025   0.282  1.00  1.00
ATOM     10  HA  ALA     1       0.023  -1.051   0.357  1.00  1.00
ATOM     11  CB  ALA     1       0.071   0.308  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.141   0.510   1.103  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.245   1.863  1.00  1.00
ATOM     17  NR  ALA     1       1.541   1.794   0.938  1.00  1.00
ATOM     18  HR  ALA     1       0.957   2.397   0.401  1.00  1.00
ATOM     19  CR  ALA     1       2.683   2.371   1.604  1.00  1.00
END
REMARK X=36 Y=37 
ATOM      1  CL  ALA     1      -3.283   1.421   1.730  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.449   1.277  1.00  1.00
ATOM      6  OL  ALA     1      -1.222   2.476   1.436  1.00  1.00
ATOM      7  NL  ALA     1      -1.405   0.299   0.773  1.00  1.00
ATOM      8  HL  ALA     1      -2.034  -0.422   0.640  1.00  1.00
ATOM      9  CA  ALA     1      -0.063   0.028   0.272  1.00  1.00
ATOM     10  HA  ALA     1       0.015  -1.050   0.307  1.00  1.00
ATOM     11  CB  ALA     1       0.057   0.364  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.134   0.492   1.093  1.00  1.00
ATOM     16  OR  ALA     1       1.729  -0.288   1.825  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.779   0.976  1.00  1.00
ATOM     18  HR  ALA     1       0.945   2.388   0.456  1.00  1.00
ATOM     19  CR  ALA     1       2.682   2.335   1.653  1.00  1.00
END
REMARK X=37 Y=38 
ATOM      1  CL  ALA     1      -3.265   1.435   1.760  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.457   1.257  1.00  1.00
ATOM      6  OL  ALA     1      -1.229   2.500   1.343  1.00  1.00
ATOM      7  NL  ALA     1      -1.398   0.292   0.802  1.00  1.00
ATOM      8  HL  ALA     1      -2.014  -0.454   0.728  1.00  1.00
ATOM      9  CA  ALA     1      -0.067   0.024   0.264  1.00  1.00
ATOM     10  HA  ALA     1       0.011  -1.049   0.257  1.00  1.00
ATOM     11  CB  ALA     1       0.028   0.426  -1.206  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.464   1.092  1.00  1.00
ATOM     16  OR  ALA     1       1.748  -0.346   1.781  1.00  1.00
ATOM     17  NR  ALA     1       1.532   1.754   1.029  1.00  1.00
ATOM     18  HR  ALA     1       0.931   2.385   0.536  1.00  1.00
ATOM     19  CR  ALA     1       2.676   2.280   1.721  1.00  1.00
END
REMARK X=38 Y=39 
ATOM      1  CL  ALA     1      -3.236   1.453   1.772  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.473   1.217  1.00  1.00
ATOM      6  OL  ALA     1      -1.244   2.522   1.222  1.00  1.00
ATOM      7  NL  ALA     1      -1.388   0.292   0.824  1.00  1.00
ATOM      8  HL  ALA     1      -1.982  -0.485   0.827  1.00  1.00
ATOM      9  CA  ALA     1      -0.066   0.031   0.248  1.00  1.00
ATOM     10  HA  ALA     1       0.018  -1.048   0.230  1.00  1.00
ATOM     11  CB  ALA     1       0.011   0.464  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.452   1.088  1.00  1.00
ATOM     16  OR  ALA     1       1.767  -0.373   1.737  1.00  1.00
ATOM     17  NR  ALA     1       1.517   1.749   1.061  1.00  1.00
ATOM     18  HR  ALA     1       0.906   2.387   0.586  1.00  1.00
ATOM     19  CR  ALA     1       2.660   2.262   1.754  1.00  1.00
END
REMARK X=39 Y=40 
ATOM      1  CL  ALA     1      -3.225   1.461   1.784  1.00  1.00
ATOM      5  CLP ALA     1      -1.878   1.466   1.191  1.00  1.00
ATOM      6  OL  ALA     1      -1.276   2.527   1.106  1.00  1.00
ATOM      7  NL  ALA     1      -1.375   0.274   0.839  1.00  1.00
ATOM      8  HL  ALA     1      -1.947  -0.517   0.921  1.00  1.00
ATOM      9  CA  ALA     1      -0.077   0.024   0.236  1.00  1.00
ATOM     10  HA  ALA     1       0.009  -1.048   0.194  1.00  1.00
ATOM     11  CB  ALA     1      -0.004   0.503  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.436   1.066  1.00  1.00
ATOM     16  OR  ALA     1       1.800  -0.403   1.678  1.00  1.00
ATOM     17  NR  ALA     1       1.483   1.736   1.091  1.00  1.00
ATOM     18  HR  ALA     1       0.861   2.388   0.647  1.00  1.00
ATOM     19  CR  ALA     1       2.642   2.246   1.792  1.00  1.00
END
REMARK X=40 Y=41 
ATOM      1  CL  ALA     1      -3.212   1.465   1.797  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.470   1.168  1.00  1.00
ATOM      6  OL  ALA     1      -1.286   2.526   1.008  1.00  1.00
ATOM      7  NL  ALA     1      -1.363   0.265   0.860  1.00  1.00
ATOM      8  HL  ALA     1      -1.914  -0.534   1.016  1.00  1.00
ATOM      9  CA  ALA     1      -0.074   0.012   0.232  1.00  1.00
ATOM     10  HA  ALA     1       0.001  -1.058   0.173  1.00  1.00
ATOM     11  CB  ALA     1      -0.020   0.528  -1.210  1.00  1.00
ATOM     15  CRP ALA     1       1.147   0.408   1.060  1.00  1.00
ATOM     16  OR  ALA     1       1.827  -0.445   1.625  1.00  1.00
ATOM     17  NR  ALA     1       1.461   1.721   1.140  1.00  1.00
ATOM     18  HR  ALA     1       0.821   2.361   0.731  1.00  1.00
ATOM     19  CR  ALA     1       2.614   2.214   1.845  1.00  1.00
END
REMARK X=41 Y=42 
ATOM      1  CL  ALA     1      -3.185   1.487   1.790  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.480   1.139  1.00  1.00
ATOM      6  OL  ALA     1      -1.293   2.532   0.896  1.00  1.00
ATOM      7  NL  ALA     1      -1.349   0.268   0.862  1.00  1.00
ATOM      8  HL  ALA     1      -1.881  -0.527   1.095  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.013   0.226  1.00  1.00
ATOM     10  HA  ALA     1      -0.006  -1.063   0.151  1.00  1.00
ATOM     11  CB  ALA     1      -0.019   0.539  -1.224  1.00  1.00
ATOM     15  CRP ALA     1       1.170   0.398   1.031  1.00  1.00
ATOM     16  OR  ALA     1       1.871  -0.463   1.540  1.00  1.00
ATOM     17  NR  ALA     1       1.447   1.706   1.159  1.00  1.00
ATOM     18  HR  ALA     1       0.788   2.362   0.800  1.00  1.00
ATOM     19  CR  ALA     1       2.602   2.205   1.868  1.00  1.00
END
REMARK X=42 Y=43 
ATOM      1  CL  ALA     1      -3.257   1.605   1.105  1.00  1.00
ATOM      5  CLP ALA     1      -1.941   1.459   0.447  1.00  1.00
ATOM      6  OL  ALA     1      -1.481   2.369  -0.223  1.00  1.00
ATOM      7  NL  ALA     1      -1.303   0.291   0.647  1.00  1.00
ATOM      8  HL  ALA     1      -1.743  -0.379   1.229  1.00  1.00
ATOM      9  CA  ALA     1      -0.011  -0.077   0.099  1.00  1.00
ATOM     10  HA  ALA     1       0.155  -1.099   0.417  1.00  1.00
ATOM     11  CB  ALA     1       0.001  -0.097  -1.439  1.00  1.00
ATOM     15  CRP ALA     1       1.191   0.673   0.683  1.00  1.00
ATOM     16  OR  ALA     1       2.015   0.103   1.375  1.00  1.00
ATOM     17  NR  ALA     1       1.303   1.983   0.393  1.00  1.00
ATOM     18  HR  ALA     1       0.553   2.411  -0.109  1.00  1.00
ATOM     19  CR  ALA     1       2.395   2.811   0.843  1.00  1.00
END
FIXED
  
 NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1,5,6,7,8,9,10,11,15,16,17,18,19
The WHOLEMOLECULES action with label  calculates somethingrmsd_cposThe POSITION action with label rmsd_cpos calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd_cpos.x
vector
the x-component of the atom position
rmsd_cpos.y
vector
the y-component of the atom position
rmsd_cpos.z
vector
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMSthe atom numbers that you would like to use the positions of=1,5,6,7,8,9,10,11,15,16,17,18,19
rmsd_posThe CONCATENATE action with label rmsd_pos calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd_pos
vector
the concatenated vector/matrix that was constructed from the input values: CONCATENATEJoin vectors or matrices together More details ARGthe values that should be concatenated together to form the output vector=rmsd_cpos.x,rmsd_cpos.y,rmsd_cpos.z
rmsdThe RMSD action with label rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd
vector
a vector containing the RMSD between the instantaneous structure and each of the reference structures that were input: RMSDCalculate the RMSD with respect to a reference structure. More details ARGinstead of using the REFERENCE option you can use this action to specify the labels of two actions that you are calculating the RMSD between=rmsd_pos,rmsd_ref ALIGN the weights to use when aligning to the reference structure=1,1,1,1,1,1,1,1,1,1,1,1,1 DISPLACE the weights to use when calculating the displacement from the reference structure=1,1,1,1,1,1,1,1,1,1,1,1,1 SQUARED  This should be setted if you want MSD instead of RMSD  TYPE the manner in which RMSD alignment is performed=OPTIMAL
# --- End of included input --- 
# The weights of the landmarks
weightsThe ONES action with label weights calculates the following quantities:
 Quantity   
 Type   
 Description  
weights
vector
a vector of ones with the required number of elements: ONESCreate a constant vector with all elements equal to one This action is a shortcut. More details SIZEthe number of ones that you would like to create=42
# PLUMED interprets the command:
# weights: ONES SIZE=42
# as follows (Click the red comment above to revert to the short version of the input):
weightsThe CONSTANT action with label weights calculates the following quantities:
 Quantity   
 Type   
 Description  
weights
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details NOLOG do not report all the read in scalars in the log VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
# --- End of included input --- 
# The projections of the landmarks in the low dimensional space
XThe PDB2CONSTANT action with label X calculates the following quantities:
 Quantity   
 Type   
 Description  
X
vector
a value that is constructed from the information in the PDB file: PDB2CONSTANTCreate a constant value from a PDB input file This action is a shortcut and it has hidden defaults. More details ARGread this single argument from the input rather than the atomic structure=X NOARGS the arguments that are being read from the PDB file are not in the plumed input REFERENCEa file in pdb format containing the reference structure=
regtest/trajectories/path_msd/allv.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/trajectories/path_msd/allv.pdb
    
REMARK X=1 Y=2 
ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00
ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00
ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00
ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00
ATOM      8  HL  ALA     1      -1.845   0.961  -0.011  1.00  1.00
ATOM      9  CA  ALA     1      -0.003  -0.019   0.021  1.00  1.00
ATOM     10  HA  ALA     1       0.205  -1.051   0.259  1.00  1.00
ATOM     11  CB  ALA     1       0.009   0.135  -1.509  1.00  1.00
ATOM     15  CRP ALA     1       1.121   0.799   0.663  1.00  1.00
ATOM     16  OR  ALA     1       1.723   1.669   0.043  1.00  1.00
ATOM     17  NR  ALA     1       1.423   0.519   1.941  1.00  1.00
ATOM     18  HR  ALA     1       0.873  -0.161   2.413  1.00  1.00
ATOM     19  CR  ALA     1       2.477   1.187   2.675  1.00  1.00
END
FIXED
REMARK X=2 Y=3 
ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00
ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00
ATOM      6  OL  ALA     1      -1.201  -0.849   2.425  1.00  1.00
ATOM      7  NL  ALA     1      -1.296   0.337   0.534  1.00  1.00
ATOM      8  HL  ALA     1      -1.807   0.951  -0.044  1.00  1.00
ATOM      9  CA  ALA     1       0.009  -0.067   0.033  1.00  1.00
ATOM     10  HA  ALA     1       0.175  -1.105   0.283  1.00  1.00
ATOM     11  CB  ALA     1       0.027   0.046  -1.501  1.00  1.00
ATOM     15  CRP ALA     1       1.149   0.725   0.654  1.00  1.00
ATOM     16  OR  ALA     1       1.835   1.491  -0.011  1.00  1.00
ATOM     17  NR  ALA     1       1.380   0.537   1.968  1.00  1.00
ATOM     18  HR  ALA     1       0.764  -0.060   2.461  1.00  1.00
ATOM     19  CR  ALA     1       2.431   1.195   2.683  1.00  1.00
END
REMARK X=3 Y=4 
ATOM      1  CL  ALA     1      -2.990   0.383   2.277  1.00  1.00
ATOM      5  CLP ALA     1      -1.664  -0.085   1.831  1.00  1.00
ATOM      6  OL  ALA     1      -0.987  -0.835   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.227   0.364   0.646  1.00  1.00
ATOM      8  HL  ALA     1      -1.798   0.982   0.124  1.00  1.00
ATOM      9  CA  ALA     1       0.026  -0.028   0.044  1.00  1.00
ATOM     10  HA  ALA     1       0.224  -1.060   0.284  1.00  1.00
ATOM     11  CB  ALA     1      -0.076   0.107  -1.483  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.776   0.577  1.00  1.00
ATOM     16  OR  ALA     1       1.900   1.463  -0.158  1.00  1.00
ATOM     17  NR  ALA     1       1.494   0.666   1.888  1.00  1.00
ATOM     18  HR  ALA     1       0.882   0.122   2.437  1.00  1.00
ATOM     19  CR  ALA     1       2.580   1.341   2.529  1.00  1.00
END
REMARK X=4 Y=5 
ATOM      1  CL  ALA     1      -3.006   0.350   2.252  1.00  1.00
ATOM      5  CLP ALA     1      -1.680  -0.112   1.826  1.00  1.00
ATOM      6  OL  ALA     1      -1.025  -0.896   2.508  1.00  1.00
ATOM      7  NL  ALA     1      -1.220   0.368   0.654  1.00  1.00
ATOM      8  HL  ALA     1      -1.771   1.013   0.137  1.00  1.00
ATOM      9  CA  ALA     1       0.040  -0.029   0.062  1.00  1.00
ATOM     10  HA  ALA     1       0.210  -1.076   0.277  1.00  1.00
ATOM     11  CB  ALA     1      -0.066   0.148  -1.465  1.00  1.00
ATOM     15  CRP ALA     1       1.241   0.738   0.605  1.00  1.00
ATOM     16  OR  ALA     1       1.986   1.347  -0.125  1.00  1.00
ATOM     17  NR  ALA     1       1.446   0.694   1.940  1.00  1.00
ATOM     18  HR  ALA     1       0.796   0.210   2.481  1.00  1.00
ATOM     19  CR  ALA     1       2.544   1.350   2.582  1.00  1.00
END
REMARK X=5 Y=6 
ATOM      1  CL  ALA     1      -3.002   0.343   2.271  1.00  1.00
ATOM      5  CLP ALA     1      -1.672  -0.125   1.828  1.00  1.00
ATOM      6  OL  ALA     1      -1.028  -0.942   2.486  1.00  1.00
ATOM      7  NL  ALA     1      -1.213   0.373   0.670  1.00  1.00
ATOM      8  HL  ALA     1      -1.752   1.033   0.169  1.00  1.00
ATOM      9  CA  ALA     1       0.041  -0.032   0.055  1.00  1.00
ATOM     10  HA  ALA     1       0.201  -1.079   0.245  1.00  1.00
ATOM     11  CB  ALA     1      -0.079   0.194  -1.466  1.00  1.00
ATOM     15  CRP ALA     1       1.257   0.720   0.601  1.00  1.00
ATOM     16  OR  ALA     1       2.057   1.240  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.422   0.730   1.942  1.00  1.00
ATOM     18  HR  ALA     1       0.740   0.303   2.500  1.00  1.00
ATOM     19  CR  ALA     1       2.528   1.373   2.598  1.00  1.00
END
REMARK X=6 Y=7 
ATOM      1  CL  ALA     1      -3.144   1.457   1.417  1.00  1.00
ATOM      5  CLP ALA     1      -1.943   0.587   1.450  1.00  1.00
ATOM      6  OL  ALA     1      -1.588   0.028   2.480  1.00  1.00
ATOM      7  NL  ALA     1      -1.281   0.449   0.306  1.00  1.00
ATOM      8  HL  ALA     1      -1.578   0.914  -0.520  1.00  1.00
ATOM      9  CA  ALA     1      -0.132  -0.428   0.139  1.00  1.00
ATOM     10  HA  ALA     1      -0.264  -1.291   0.758  1.00  1.00
ATOM     11  CB  ALA     1      -0.066  -0.855  -1.329  1.00  1.00
ATOM     15  CRP ALA     1       1.193   0.220   0.554  1.00  1.00
ATOM     16  OR  ALA     1       2.195   0.098  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.224   0.872   1.737  1.00  1.00
ATOM     18  HR  ALA     1       0.399   0.943   2.273  1.00  1.00
ATOM     19  CR  ALA     1       2.413   1.511   2.254  1.00  1.00
END
REMARK X=7 Y=8 
ATOM      1  CL  ALA     1      -3.140   1.441   1.453  1.00  1.00
ATOM      5  CLP ALA     1      -1.944   0.576   1.465  1.00  1.00
ATOM      6  OL  ALA     1      -1.587  -0.018   2.487  1.00  1.00
ATOM      7  NL  ALA     1      -1.274   0.465   0.322  1.00  1.00
ATOM      8  HL  ALA     1      -1.571   0.957  -0.486  1.00  1.00
ATOM      9  CA  ALA     1      -0.124  -0.418   0.135  1.00  1.00
ATOM     10  HA  ALA     1      -0.274  -1.304   0.729  1.00  1.00
ATOM     11  CB  ALA     1      -0.063  -0.813  -1.347  1.00  1.00
ATOM     15  CRP ALA     1       1.201   0.199   0.572  1.00  1.00
ATOM     16  OR  ALA     1       2.227   0.007  -0.072  1.00  1.00
ATOM     17  NR  ALA     1       1.215   0.910   1.709  1.00  1.00
ATOM     18  HR  ALA     1       0.369   1.020   2.200  1.00  1.00
ATOM     19  CR  ALA     1       2.393   1.536   2.237  1.00  1.00
END
REMARK X=8 Y=9 
ATOM      1  CL  ALA     1      -3.140   1.420   1.442  1.00  1.00
ATOM      5  CLP ALA     1      -1.948   0.546   1.448  1.00  1.00
ATOM      6  OL  ALA     1      -1.618  -0.065   2.460  1.00  1.00
ATOM      7  NL  ALA     1      -1.255   0.469   0.311  1.00  1.00
ATOM      8  HL  ALA     1      -1.538   0.979  -0.490  1.00  1.00
ATOM      9  CA  ALA     1      -0.107  -0.412   0.124  1.00  1.00
ATOM     10  HA  ALA     1      -0.257  -1.312   0.685  1.00  1.00
ATOM     11  CB  ALA     1      -0.028  -0.770  -1.375  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.186   0.600  1.00  1.00
ATOM     16  OR  ALA     1       2.269  -0.069   0.026  1.00  1.00
ATOM     17  NR  ALA     1       1.193   0.966   1.687  1.00  1.00
ATOM     18  HR  ALA     1       0.333   1.114   2.120  1.00  1.00
ATOM     19  CR  ALA     1       2.377   1.589   2.240  1.00  1.00
END
REMARK X=9 Y=10 
ATOM      1  CL  ALA     1      -3.110   1.698   0.880  1.00  1.00
ATOM      5  CLP ALA     1      -2.021   0.734   1.142  1.00  1.00
ATOM      6  OL  ALA     1      -1.859   0.257   2.258  1.00  1.00
ATOM      7  NL  ALA     1      -1.229   0.414   0.114  1.00  1.00
ATOM      8  HL  ALA     1      -1.371   0.826  -0.771  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.593   0.188  1.00  1.00
ATOM     10  HA  ALA     1      -0.481  -1.374   0.851  1.00  1.00
ATOM     11  CB  ALA     1       0.011  -1.180  -1.220  1.00  1.00
ATOM     15  CRP ALA     1       1.163  -0.060   0.716  1.00  1.00
ATOM     16  OR  ALA     1       2.227  -0.564   0.393  1.00  1.00
ATOM     17  NR  ALA     1       1.127   0.960   1.594  1.00  1.00
ATOM     18  HR  ALA     1       0.234   1.295   1.847  1.00  1.00
ATOM     19  CR  ALA     1       2.303   1.549   2.172  1.00  1.00
END
REMARK X=10 Y=11 
ATOM      1  CL  ALA     1      -3.139   1.652   0.924  1.00  1.00
ATOM      5  CLP ALA     1      -2.039   0.698   1.169  1.00  1.00
ATOM      6  OL  ALA     1      -1.868   0.201   2.278  1.00  1.00
ATOM      7  NL  ALA     1      -1.239   0.411   0.139  1.00  1.00
ATOM      8  HL  ALA     1      -1.385   0.842  -0.737  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.574   0.193  1.00  1.00
ATOM     10  HA  ALA     1      -0.477  -1.381   0.833  1.00  1.00
ATOM     11  CB  ALA     1       0.029  -1.142  -1.231  1.00  1.00
ATOM     15  CRP ALA     1       1.162  -0.048   0.731  1.00  1.00
ATOM     16  OR  ALA     1       2.220  -0.597   0.472  1.00  1.00
ATOM     17  NR  ALA     1       1.122   1.024   1.537  1.00  1.00
ATOM     18  HR  ALA     1       0.233   1.395   1.752  1.00  1.00
ATOM     19  CR  ALA     1       2.300   1.629   2.102  1.00  1.00
END
REMARK X=11 Y=12 
ATOM      1  CL  ALA     1      -3.706   1.088   0.468  1.00  1.00
ATOM      5  CLP ALA     1      -2.458   0.598   1.082  1.00  1.00
ATOM      6  OL  ALA     1      -2.390   0.404   2.277  1.00  1.00
ATOM      7  NL  ALA     1      -1.427   0.382   0.258  1.00  1.00
ATOM      8  HL  ALA     1      -1.513   0.559  -0.713  1.00  1.00
ATOM      9  CA  ALA     1      -0.157  -0.192   0.685  1.00  1.00
ATOM     10  HA  ALA     1      -0.343  -0.912   1.470  1.00  1.00
ATOM     11  CB  ALA     1       0.462  -0.936  -0.512  1.00  1.00
ATOM     15  CRP ALA     1       0.840   0.814   1.241  1.00  1.00
ATOM     16  OR  ALA     1       2.034   0.549   1.354  1.00  1.00
ATOM     17  NR  ALA     1       0.368   2.017   1.650  1.00  1.00
ATOM     18  HR  ALA     1      -0.613   2.169   1.589  1.00  1.00
ATOM     19  CR  ALA     1       1.215   3.044   2.195  1.00  1.00
END
REMARK X=12 Y=13 
ATOM      1  CL  ALA     1      -3.699   1.173   0.487  1.00  1.00
ATOM      5  CLP ALA     1      -2.464   0.631   1.079  1.00  1.00
ATOM      6  OL  ALA     1      -2.402   0.386   2.275  1.00  1.00
ATOM      7  NL  ALA     1      -1.434   0.437   0.260  1.00  1.00
ATOM      8  HL  ALA     1      -1.516   0.652  -0.701  1.00  1.00
ATOM      9  CA  ALA     1      -0.174  -0.174   0.667  1.00  1.00
ATOM     10  HA  ALA     1      -0.377  -0.924   1.411  1.00  1.00
ATOM     11  CB  ALA     1       0.451  -0.859  -0.570  1.00  1.00
ATOM     15  CRP ALA     1       0.839   0.801   1.280  1.00  1.00
ATOM     16  OR  ALA     1       1.999   0.474   1.468  1.00  1.00
ATOM     17  NR  ALA     1       0.404   2.024   1.627  1.00  1.00
ATOM     18  HR  ALA     1      -0.565   2.225   1.505  1.00  1.00
ATOM     19  CR  ALA     1       1.262   3.025   2.214  1.00  1.00
END
REMARK X=13 Y=14 
ATOM      1  CL  ALA     1      -3.653   0.990   1.121  1.00  1.00
ATOM      5  CLP ALA     1      -2.321   0.364   1.249  1.00  1.00
ATOM      6  OL  ALA     1      -2.006  -0.222   2.265  1.00  1.00
ATOM      7  NL  ALA     1      -1.498   0.501   0.205  1.00  1.00
ATOM      8  HL  ALA     1      -1.794   0.978  -0.603  1.00  1.00
ATOM      9  CA  ALA     1      -0.190  -0.127   0.128  1.00  1.00
ATOM     10  HA  ALA     1      -0.216  -1.086   0.627  1.00  1.00
ATOM     11  CB  ALA     1       0.159  -0.359  -1.359  1.00  1.00
ATOM     15  CRP ALA     1       0.933   0.668   0.793  1.00  1.00
ATOM     16  OR  ALA     1       2.107   0.313   0.705  1.00  1.00
ATOM     17  NR  ALA     1       0.604   1.770   1.498  1.00  1.00
ATOM     18  HR  ALA     1      -0.359   1.986   1.593  1.00  1.00
ATOM     19  CR  ALA     1       1.573   2.595   2.158  1.00  1.00
END
REMARK X=14 Y=15 
ATOM      1  CL  ALA     1      -3.641   0.954   1.179  1.00  1.00
ATOM      5  CLP ALA     1      -2.294   0.335   1.290  1.00  1.00
ATOM      6  OL  ALA     1      -1.964  -0.273   2.288  1.00  1.00
ATOM      7  NL  ALA     1      -1.485   0.499   0.235  1.00  1.00
ATOM      8  HL  ALA     1      -1.803   0.995  -0.564  1.00  1.00
ATOM      9  CA  ALA     1      -0.175  -0.118   0.130  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.077   0.601  1.00  1.00
ATOM     11  CB  ALA     1       0.162  -0.300  -1.355  1.00  1.00
ATOM     15  CRP ALA     1       0.952   0.671   0.815  1.00  1.00
ATOM     16  OR  ALA     1       2.104   0.260   0.791  1.00  1.00
ATOM     17  NR  ALA     1       0.633   1.808   1.450  1.00  1.00
ATOM     18  HR  ALA     1      -0.328   2.065   1.503  1.00  1.00
ATOM     19  CR  ALA     1       1.608   2.627   2.129  1.00  1.00
END
REMARK X=15 Y=16 
ATOM      1  CL  ALA     1      -3.635   0.925   1.244  1.00  1.00
ATOM      5  CLP ALA     1      -2.297   0.305   1.309  1.00  1.00
ATOM      6  OL  ALA     1      -1.941  -0.334   2.290  1.00  1.00
ATOM      7  NL  ALA     1      -1.500   0.490   0.251  1.00  1.00
ATOM      8  HL  ALA     1      -1.827   1.009  -0.537  1.00  1.00
ATOM      9  CA  ALA     1      -0.178  -0.110   0.119  1.00  1.00
ATOM     10  HA  ALA     1      -0.205  -1.094   0.536  1.00  1.00
ATOM     11  CB  ALA     1       0.147  -0.217  -1.379  1.00  1.00
ATOM     15  CRP ALA     1       0.943   0.643   0.832  1.00  1.00
ATOM     16  OR  ALA     1       2.074   0.198   0.871  1.00  1.00
ATOM     17  NR  ALA     1       0.637   1.821   1.423  1.00  1.00
ATOM     18  HR  ALA     1      -0.311   2.123   1.418  1.00  1.00
ATOM     19  CR  ALA     1       1.602   2.629   2.109  1.00  1.00
END
REMARK X=16 Y=17 
ATOM      1  CL  ALA     1      -3.632   0.856   1.331  1.00  1.00
ATOM      5  CLP ALA     1      -2.282   0.250   1.355  1.00  1.00
ATOM      6  OL  ALA     1      -1.906  -0.403   2.301  1.00  1.00
ATOM      7  NL  ALA     1      -1.515   0.478   0.275  1.00  1.00
ATOM      8  HL  ALA     1      -1.860   0.990  -0.485  1.00  1.00
ATOM      9  CA  ALA     1      -0.192  -0.105   0.098  1.00  1.00
ATOM     10  HA  ALA     1      -0.204  -1.121   0.473  1.00  1.00
ATOM     11  CB  ALA     1       0.129  -0.136  -1.408  1.00  1.00
ATOM     15  CRP ALA     1       0.931   0.615   0.844  1.00  1.00
ATOM     16  OR  ALA     1       2.043   0.122   0.934  1.00  1.00
ATOM     17  NR  ALA     1       0.651   1.819   1.388  1.00  1.00
ATOM     18  HR  ALA     1      -0.283   2.155   1.349  1.00  1.00
ATOM     19  CR  ALA     1       1.624   2.595   2.115  1.00  1.00
END
REMARK X=17 Y=18 
ATOM      1  CL  ALA     1      -3.628   0.823   1.358  1.00  1.00
ATOM      5  CLP ALA     1      -2.277   0.241   1.370  1.00  1.00
ATOM      6  OL  ALA     1      -1.871  -0.396   2.325  1.00  1.00
ATOM      7  NL  ALA     1      -1.525   0.469   0.284  1.00  1.00
ATOM      8  HL  ALA     1      -1.898   0.970  -0.482  1.00  1.00
ATOM      9  CA  ALA     1      -0.195  -0.094   0.086  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.122   0.423  1.00  1.00
ATOM     11  CB  ALA     1       0.146  -0.058  -1.413  1.00  1.00
ATOM     15  CRP ALA     1       0.919   0.599   0.874  1.00  1.00
ATOM     16  OR  ALA     1       1.997   0.065   1.039  1.00  1.00
ATOM     17  NR  ALA     1       0.655   1.830   1.373  1.00  1.00
ATOM     18  HR  ALA     1      -0.248   2.200   1.261  1.00  1.00
ATOM     19  CR  ALA     1       1.625   2.581   2.124  1.00  1.00
END
REMARK X=18 Y=19 
ATOM      1  CL  ALA     1      -3.539   0.055   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -2.117  -0.208   1.378  1.00  1.00
ATOM      6  OL  ALA     1      -1.453  -0.902   2.125  1.00  1.00
ATOM      7  NL  ALA     1      -1.602   0.351   0.289  1.00  1.00
ATOM      8  HL  ALA     1      -2.185   0.875  -0.310  1.00  1.00
ATOM      9  CA  ALA     1      -0.243   0.129  -0.186  1.00  1.00
ATOM     10  HA  ALA     1      -0.041  -0.924  -0.159  1.00  1.00
ATOM     11  CB  ALA     1      -0.153   0.625  -1.651  1.00  1.00
ATOM     15  CRP ALA     1       0.852   0.806   0.637  1.00  1.00
ATOM     16  OR  ALA     1       2.007   0.400   0.594  1.00  1.00
ATOM     17  NR  ALA     1       0.508   1.855   1.401  1.00  1.00
ATOM     18  HR  ALA     1      -0.445   2.112   1.454  1.00  1.00
ATOM     19  CR  ALA     1       1.460   2.569   2.226  1.00  1.00
END
REMARK X=19 Y=20 
ATOM      1  CL  ALA     1      -3.578   0.084   1.603  1.00  1.00
ATOM      5  CLP ALA     1      -2.140  -0.156   1.375  1.00  1.00
ATOM      6  OL  ALA     1      -1.473  -0.732   2.197  1.00  1.00
ATOM      7  NL  ALA     1      -1.623   0.335   0.237  1.00  1.00
ATOM      8  HL  ALA     1      -2.220   0.753  -0.416  1.00  1.00
ATOM      9  CA  ALA     1      -0.253   0.120  -0.195  1.00  1.00
ATOM     10  HA  ALA     1      -0.048  -0.931  -0.153  1.00  1.00
ATOM     11  CB  ALA     1      -0.128   0.612  -1.663  1.00  1.00
ATOM     15  CRP ALA     1       0.823   0.801   0.637  1.00  1.00
ATOM     16  OR  ALA     1       1.969   0.367   0.665  1.00  1.00
ATOM     17  NR  ALA     1       0.477   1.912   1.333  1.00  1.00
ATOM     18  HR  ALA     1      -0.468   2.199   1.317  1.00  1.00
ATOM     19  CR  ALA     1       1.410   2.627   2.163  1.00  1.00
END
REMARK X=20 Y=21 
ATOM      1  CL  ALA     1      -3.113   1.661   1.504  1.00  1.00
ATOM      5  CLP ALA     1      -1.769   1.059   1.566  1.00  1.00
ATOM      6  OL  ALA     1      -1.201   0.940   2.629  1.00  1.00
ATOM      7  NL  ALA     1      -1.219   0.714   0.392  1.00  1.00
ATOM      8  HL  ALA     1      -1.742   0.797  -0.435  1.00  1.00
ATOM      9  CA  ALA     1       0.058   0.023   0.242  1.00  1.00
ATOM     10  HA  ALA     1      -0.001  -0.896   0.782  1.00  1.00
ATOM     11  CB  ALA     1       0.235  -0.295  -1.249  1.00  1.00
ATOM     15  CRP ALA     1       1.299   0.757   0.745  1.00  1.00
ATOM     16  OR  ALA     1       2.276   0.138   1.135  1.00  1.00
ATOM     17  NR  ALA     1       1.277   2.102   0.736  1.00  1.00
ATOM     18  HR  ALA     1       0.447   2.567   0.458  1.00  1.00
ATOM     19  CR  ALA     1       2.391   2.896   1.191  1.00  1.00
END
REMARK X=21 Y=22 
ATOM      1  CL  ALA     1      -3.089   1.850   1.546  1.00  1.00
ATOM      5  CLP ALA     1      -1.667   1.457   1.629  1.00  1.00
ATOM      6  OL  ALA     1      -0.974   1.868   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.204   0.683   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -1.844   0.360  -0.021  1.00  1.00
ATOM      9  CA  ALA     1       0.126   0.105   0.564  1.00  1.00
ATOM     10  HA  ALA     1       0.239  -0.555   1.391  1.00  1.00
ATOM     11  CB  ALA     1       0.215  -0.722  -0.739  1.00  1.00
ATOM     15  CRP ALA     1       1.311   1.068   0.623  1.00  1.00
ATOM     16  OR  ALA     1       2.369   0.726   1.149  1.00  1.00
ATOM     17  NR  ALA     1       1.156   2.292   0.077  1.00  1.00
ATOM     18  HR  ALA     1       0.273   2.549  -0.285  1.00  1.00
ATOM     19  CR  ALA     1       2.201   3.277   0.107  1.00  1.00
END
REMARK X=22 Y=23 
ATOM      1  CL  ALA     1      -3.102   1.775   1.619  1.00  1.00
ATOM      5  CLP ALA     1      -1.661   1.466   1.659  1.00  1.00
ATOM      6  OL  ALA     1      -0.945   1.961   2.476  1.00  1.00
ATOM      7  NL  ALA     1      -1.205   0.663   0.688  1.00  1.00
ATOM      8  HL  ALA     1      -1.854   0.269   0.091  1.00  1.00
ATOM      9  CA  ALA     1       0.147   0.134   0.561  1.00  1.00
ATOM     10  HA  ALA     1       0.300  -0.545   1.355  1.00  1.00
ATOM     11  CB  ALA     1       0.237  -0.632  -0.776  1.00  1.00
ATOM     15  CRP ALA     1       1.306   1.133   0.628  1.00  1.00
ATOM     16  OR  ALA     1       2.361   0.819   1.176  1.00  1.00
ATOM     17  NR  ALA     1       1.129   2.345   0.068  1.00  1.00
ATOM     18  HR  ALA     1       0.252   2.577  -0.315  1.00  1.00
ATOM     19  CR  ALA     1       2.150   3.364   0.108  1.00  1.00
END
REMARK X=23 Y=24 
ATOM      1  CL  ALA     1      -3.137   1.689   1.564  1.00  1.00
ATOM      5  CLP ALA     1      -1.674   1.466   1.595  1.00  1.00
ATOM      6  OL  ALA     1      -0.991   2.041   2.377  1.00  1.00
ATOM      7  NL  ALA     1      -1.178   0.640   0.664  1.00  1.00
ATOM      8  HL  ALA     1      -1.829   0.190   0.106  1.00  1.00
ATOM      9  CA  ALA     1       0.192   0.170   0.547  1.00  1.00
ATOM     10  HA  ALA     1       0.347  -0.550   1.313  1.00  1.00
ATOM     11  CB  ALA     1       0.333  -0.536  -0.821  1.00  1.00
ATOM     15  CRP ALA     1       1.325   1.194   0.686  1.00  1.00
ATOM     16  OR  ALA     1       2.348   0.906   1.293  1.00  1.00
ATOM     17  NR  ALA     1       1.165   2.398   0.103  1.00  1.00
ATOM     18  HR  ALA     1       0.311   2.617  -0.339  1.00  1.00
ATOM     19  CR  ALA     1       2.173   3.424   0.206  1.00  1.00
END
REMARK X=24 Y=25 
ATOM      1  CL  ALA     1      -3.342   1.726   1.297  1.00  1.00
ATOM      5  CLP ALA     1      -1.882   1.644   1.449  1.00  1.00
ATOM      6  OL  ALA     1      -1.296   2.423   2.124  1.00  1.00
ATOM      7  NL  ALA     1      -1.259   0.684   0.740  1.00  1.00
ATOM      8  HL  ALA     1      -1.839   0.091   0.256  1.00  1.00
ATOM      9  CA  ALA     1       0.138   0.295   0.784  1.00  1.00
ATOM     10  HA  ALA     1       0.267  -0.321   1.638  1.00  1.00
ATOM     11  CB  ALA     1       0.437  -0.541  -0.481  1.00  1.00
ATOM     15  CRP ALA     1       1.207   1.385   0.899  1.00  1.00
ATOM     16  OR  ALA     1       2.160   1.248   1.674  1.00  1.00
ATOM     17  NR  ALA     1       1.092   2.478   0.129  1.00  1.00
ATOM     18  HR  ALA     1       0.291   2.586  -0.440  1.00  1.00
ATOM     19  CR  ALA     1       2.044   3.567   0.190  1.00  1.00
END
REMARK X=25 Y=26 
ATOM      1  CL  ALA     1      -3.361   1.726   1.315  1.00  1.00
ATOM      5  CLP ALA     1      -1.890   1.687   1.423  1.00  1.00
ATOM      6  OL  ALA     1      -1.302   2.522   2.029  1.00  1.00
ATOM      7  NL  ALA     1      -1.285   0.691   0.757  1.00  1.00
ATOM      8  HL  ALA     1      -1.865   0.049   0.326  1.00  1.00
ATOM      9  CA  ALA     1       0.123   0.321   0.749  1.00  1.00
ATOM     10  HA  ALA     1       0.270  -0.331   1.585  1.00  1.00
ATOM     11  CB  ALA     1       0.408  -0.470  -0.534  1.00  1.00
ATOM     15  CRP ALA     1       1.192   1.410   0.900  1.00  1.00
ATOM     16  OR  ALA     1       2.114   1.273   1.701  1.00  1.00
ATOM     17  NR  ALA     1       1.111   2.493   0.112  1.00  1.00
ATOM     18  HR  ALA     1       0.326   2.609  -0.490  1.00  1.00
ATOM     19  CR  ALA     1       2.068   3.578   0.188  1.00  1.00
END
REMARK X=26 Y=27 
ATOM      1  CL  ALA     1      -3.419   1.747   1.251  1.00  1.00
ATOM      5  CLP ALA     1      -1.947   1.630   1.371  1.00  1.00
ATOM      6  OL  ALA     1      -1.331   2.379   2.060  1.00  1.00
ATOM      7  NL  ALA     1      -1.380   0.668   0.616  1.00  1.00
ATOM      8  HL  ALA     1      -1.992   0.115   0.104  1.00  1.00
ATOM      9  CA  ALA     1       0.007   0.227   0.571  1.00  1.00
ATOM     10  HA  ALA     1       0.086  -0.578   1.262  1.00  1.00
ATOM     11  CB  ALA     1       0.288  -0.306  -0.835  1.00  1.00
ATOM     15  CRP ALA     1       1.132   1.190   0.974  1.00  1.00
ATOM     16  OR  ALA     1       1.974   0.858   1.808  1.00  1.00
ATOM     17  NR  ALA     1       1.199   2.390   0.352  1.00  1.00
ATOM     18  HR  ALA     1       0.482   2.643  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.218   3.363   0.657  1.00  1.00
END
REMARK X=27 Y=28 
ATOM      1  CL  ALA     1      -3.430   1.748   1.261  1.00  1.00
ATOM      5  CLP ALA     1      -1.958   1.650   1.340  1.00  1.00
ATOM      6  OL  ALA     1      -1.333   2.471   1.961  1.00  1.00
ATOM      7  NL  ALA     1      -1.392   0.653   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -2.018   0.061   0.177  1.00  1.00
ATOM      9  CA  ALA     1      -0.005   0.219   0.569  1.00  1.00
ATOM     10  HA  ALA     1       0.083  -0.615   1.230  1.00  1.00
ATOM     11  CB  ALA     1       0.266  -0.275  -0.863  1.00  1.00
ATOM     15  CRP ALA     1       1.126   1.166   0.993  1.00  1.00
ATOM     16  OR  ALA     1       1.918   0.834   1.868  1.00  1.00
ATOM     17  NR  ALA     1       1.248   2.346   0.359  1.00  1.00
ATOM     18  HR  ALA     1       0.548   2.609  -0.299  1.00  1.00
ATOM     19  CR  ALA     1       2.271   3.308   0.675  1.00  1.00
END
REMARK X=28 Y=29 
ATOM      1  CL  ALA     1      -3.438   1.702   1.306  1.00  1.00
ATOM      5  CLP ALA     1      -1.962   1.659   1.317  1.00  1.00
ATOM      6  OL  ALA     1      -1.332   2.532   1.870  1.00  1.00
ATOM      7  NL  ALA     1      -1.406   0.632   0.671  1.00  1.00
ATOM      8  HL  ALA     1      -2.029   0.002   0.252  1.00  1.00
ATOM      9  CA  ALA     1      -0.007   0.228   0.554  1.00  1.00
ATOM     10  HA  ALA     1       0.103  -0.631   1.184  1.00  1.00
ATOM     11  CB  ALA     1       0.255  -0.224  -0.899  1.00  1.00
ATOM     15  CRP ALA     1       1.124   1.169   1.002  1.00  1.00
ATOM     16  OR  ALA     1       1.889   0.829   1.901  1.00  1.00
ATOM     17  NR  ALA     1       1.265   2.342   0.365  1.00  1.00
ATOM     18  HR  ALA     1       0.590   2.614  -0.306  1.00  1.00
ATOM     19  CR  ALA     1       2.313   3.280   0.698  1.00  1.00
END
REMARK X=29 Y=30 
ATOM      1  CL  ALA     1      -3.441   1.677   1.342  1.00  1.00
ATOM      5  CLP ALA     1      -1.971   1.666   1.304  1.00  1.00
ATOM      6  OL  ALA     1      -1.348   2.594   1.774  1.00  1.00
ATOM      7  NL  ALA     1      -1.408   0.602   0.696  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.062   0.329  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.235   0.538  1.00  1.00
ATOM     10  HA  ALA     1       0.114  -0.660   1.127  1.00  1.00
ATOM     11  CB  ALA     1       0.223  -0.161  -0.935  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.153   1.020  1.00  1.00
ATOM     16  OR  ALA     1       1.857   0.813   1.931  1.00  1.00
ATOM     17  NR  ALA     1       1.290   2.335   0.385  1.00  1.00
ATOM     18  HR  ALA     1       0.632   2.617  -0.298  1.00  1.00
ATOM     19  CR  ALA     1       2.337   3.252   0.749  1.00  1.00
END
REMARK X=30 Y=31 
ATOM      1  CL  ALA     1      -3.443   1.670   1.352  1.00  1.00
ATOM      5  CLP ALA     1      -1.973   1.670   1.295  1.00  1.00
ATOM      6  OL  ALA     1      -1.351   2.609   1.744  1.00  1.00
ATOM      7  NL  ALA     1      -1.409   0.597   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.076   0.355  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.237   0.533  1.00  1.00
ATOM     10  HA  ALA     1       0.119  -0.663   1.113  1.00  1.00
ATOM     11  CB  ALA     1       0.217  -0.147  -0.945  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.152   1.023  1.00  1.00
ATOM     16  OR  ALA     1       1.849   0.808   1.938  1.00  1.00
ATOM     17  NR  ALA     1       1.296   2.334   0.388  1.00  1.00
ATOM     18  HR  ALA     1       0.638   2.620  -0.293  1.00  1.00
ATOM     19  CR  ALA     1       2.342   3.249   0.754  1.00  1.00
END
REMARK X=31 Y=32 
ATOM      1  CL  ALA     1      -3.451   1.630   1.422  1.00  1.00
ATOM      5  CLP ALA     1      -1.983   1.689   1.248  1.00  1.00
ATOM      6  OL  ALA     1      -1.374   2.689   1.550  1.00  1.00
ATOM      7  NL  ALA     1      -1.421   0.569   0.756  1.00  1.00
ATOM      8  HL  ALA     1      -2.045  -0.151   0.513  1.00  1.00
ATOM      9  CA  ALA     1      -0.017   0.248   0.499  1.00  1.00
ATOM     10  HA  ALA     1       0.149  -0.681   1.023  1.00  1.00
ATOM     11  CB  ALA     1       0.171  -0.057  -0.999  1.00  1.00
ATOM     15  CRP ALA     1       1.111   1.147   1.033  1.00  1.00
ATOM     16  OR  ALA     1       1.807   0.781   1.969  1.00  1.00
ATOM     17  NR  ALA     1       1.327   2.329   0.410  1.00  1.00
ATOM     18  HR  ALA     1       0.679   2.635  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.372   3.237   0.799  1.00  1.00
END
REMARK X=32 Y=33 
ATOM      1  CL  ALA     1      -3.331   1.449   1.617  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.399   1.408  1.00  1.00
ATOM      6  OL  ALA     1      -1.169   2.255   1.904  1.00  1.00
ATOM      7  NL  ALA     1      -1.424   0.371   0.676  1.00  1.00
ATOM      8  HL  ALA     1      -2.118  -0.203   0.289  1.00  1.00
ATOM      9  CA  ALA     1      -0.062   0.001   0.310  1.00  1.00
ATOM     10  HA  ALA     1      -0.008  -1.054   0.497  1.00  1.00
ATOM     11  CB  ALA     1       0.131   0.162  -1.216  1.00  1.00
ATOM     15  CRP ALA     1       1.142   0.546   1.099  1.00  1.00
ATOM     16  OR  ALA     1       1.741  -0.171   1.894  1.00  1.00
ATOM     17  NR  ALA     1       1.537   1.815   0.864  1.00  1.00
ATOM     18  HR  ALA     1       0.963   2.391   0.297  1.00  1.00
ATOM     19  CR  ALA     1       2.669   2.426   1.513  1.00  1.00
END
REMARK X=33 Y=34 
ATOM      1  CL  ALA     1      -3.321   1.436   1.650  1.00  1.00
ATOM      5  CLP ALA     1      -1.870   1.422   1.372  1.00  1.00
ATOM      6  OL  ALA     1      -1.182   2.323   1.789  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.347   0.697  1.00  1.00
ATOM      8  HL  ALA     1      -2.106  -0.263   0.374  1.00  1.00
ATOM      9  CA  ALA     1      -0.057   0.008   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.002  -1.051   0.446  1.00  1.00
ATOM     11  CB  ALA     1       0.113   0.213  -1.212  1.00  1.00
ATOM     15  CRP ALA     1       1.139   0.538   1.102  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.196   1.881  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.803   0.879  1.00  1.00
ATOM     18  HR  ALA     1       0.972   2.397   0.326  1.00  1.00
ATOM     19  CR  ALA     1       2.672   2.407   1.539  1.00  1.00
END
REMARK X=34 Y=35 
ATOM      1  CL  ALA     1      -3.318   1.434   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -1.871   1.426   1.363  1.00  1.00
ATOM      6  OL  ALA     1      -1.186   2.341   1.756  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.343   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.101  -0.279   0.398  1.00  1.00
ATOM      9  CA  ALA     1      -0.058   0.010   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.005  -1.051   0.433  1.00  1.00
ATOM     11  CB  ALA     1       0.109   0.227  -1.215  1.00  1.00
ATOM     15  CRP ALA     1       1.138   0.536   1.100  1.00  1.00
ATOM     16  OR  ALA     1       1.723  -0.202   1.878  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.802   0.887  1.00  1.00
ATOM     18  HR  ALA     1       0.970   2.398   0.335  1.00  1.00
ATOM     19  CR  ALA     1       2.675   2.402   1.547  1.00  1.00
END
REMARK X=35 Y=36 
ATOM      1  CL  ALA     1      -3.297   1.417   1.700  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.437   1.310  1.00  1.00
ATOM      6  OL  ALA     1      -1.214   2.432   1.560  1.00  1.00
ATOM      7  NL  ALA     1      -1.412   0.320   0.746  1.00  1.00
ATOM      8  HL  ALA     1      -2.060  -0.372   0.544  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.025   0.282  1.00  1.00
ATOM     10  HA  ALA     1       0.023  -1.051   0.357  1.00  1.00
ATOM     11  CB  ALA     1       0.071   0.308  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.141   0.510   1.103  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.245   1.863  1.00  1.00
ATOM     17  NR  ALA     1       1.541   1.794   0.938  1.00  1.00
ATOM     18  HR  ALA     1       0.957   2.397   0.401  1.00  1.00
ATOM     19  CR  ALA     1       2.683   2.371   1.604  1.00  1.00
END
REMARK X=36 Y=37 
ATOM      1  CL  ALA     1      -3.283   1.421   1.730  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.449   1.277  1.00  1.00
ATOM      6  OL  ALA     1      -1.222   2.476   1.436  1.00  1.00
ATOM      7  NL  ALA     1      -1.405   0.299   0.773  1.00  1.00
ATOM      8  HL  ALA     1      -2.034  -0.422   0.640  1.00  1.00
ATOM      9  CA  ALA     1      -0.063   0.028   0.272  1.00  1.00
ATOM     10  HA  ALA     1       0.015  -1.050   0.307  1.00  1.00
ATOM     11  CB  ALA     1       0.057   0.364  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.134   0.492   1.093  1.00  1.00
ATOM     16  OR  ALA     1       1.729  -0.288   1.825  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.779   0.976  1.00  1.00
ATOM     18  HR  ALA     1       0.945   2.388   0.456  1.00  1.00
ATOM     19  CR  ALA     1       2.682   2.335   1.653  1.00  1.00
END
REMARK X=37 Y=38 
ATOM      1  CL  ALA     1      -3.265   1.435   1.760  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.457   1.257  1.00  1.00
ATOM      6  OL  ALA     1      -1.229   2.500   1.343  1.00  1.00
ATOM      7  NL  ALA     1      -1.398   0.292   0.802  1.00  1.00
ATOM      8  HL  ALA     1      -2.014  -0.454   0.728  1.00  1.00
ATOM      9  CA  ALA     1      -0.067   0.024   0.264  1.00  1.00
ATOM     10  HA  ALA     1       0.011  -1.049   0.257  1.00  1.00
ATOM     11  CB  ALA     1       0.028   0.426  -1.206  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.464   1.092  1.00  1.00
ATOM     16  OR  ALA     1       1.748  -0.346   1.781  1.00  1.00
ATOM     17  NR  ALA     1       1.532   1.754   1.029  1.00  1.00
ATOM     18  HR  ALA     1       0.931   2.385   0.536  1.00  1.00
ATOM     19  CR  ALA     1       2.676   2.280   1.721  1.00  1.00
END
REMARK X=38 Y=39 
ATOM      1  CL  ALA     1      -3.236   1.453   1.772  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.473   1.217  1.00  1.00
ATOM      6  OL  ALA     1      -1.244   2.522   1.222  1.00  1.00
ATOM      7  NL  ALA     1      -1.388   0.292   0.824  1.00  1.00
ATOM      8  HL  ALA     1      -1.982  -0.485   0.827  1.00  1.00
ATOM      9  CA  ALA     1      -0.066   0.031   0.248  1.00  1.00
ATOM     10  HA  ALA     1       0.018  -1.048   0.230  1.00  1.00
ATOM     11  CB  ALA     1       0.011   0.464  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.452   1.088  1.00  1.00
ATOM     16  OR  ALA     1       1.767  -0.373   1.737  1.00  1.00
ATOM     17  NR  ALA     1       1.517   1.749   1.061  1.00  1.00
ATOM     18  HR  ALA     1       0.906   2.387   0.586  1.00  1.00
ATOM     19  CR  ALA     1       2.660   2.262   1.754  1.00  1.00
END
REMARK X=39 Y=40 
ATOM      1  CL  ALA     1      -3.225   1.461   1.784  1.00  1.00
ATOM      5  CLP ALA     1      -1.878   1.466   1.191  1.00  1.00
ATOM      6  OL  ALA     1      -1.276   2.527   1.106  1.00  1.00
ATOM      7  NL  ALA     1      -1.375   0.274   0.839  1.00  1.00
ATOM      8  HL  ALA     1      -1.947  -0.517   0.921  1.00  1.00
ATOM      9  CA  ALA     1      -0.077   0.024   0.236  1.00  1.00
ATOM     10  HA  ALA     1       0.009  -1.048   0.194  1.00  1.00
ATOM     11  CB  ALA     1      -0.004   0.503  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.436   1.066  1.00  1.00
ATOM     16  OR  ALA     1       1.800  -0.403   1.678  1.00  1.00
ATOM     17  NR  ALA     1       1.483   1.736   1.091  1.00  1.00
ATOM     18  HR  ALA     1       0.861   2.388   0.647  1.00  1.00
ATOM     19  CR  ALA     1       2.642   2.246   1.792  1.00  1.00
END
REMARK X=40 Y=41 
ATOM      1  CL  ALA     1      -3.212   1.465   1.797  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.470   1.168  1.00  1.00
ATOM      6  OL  ALA     1      -1.286   2.526   1.008  1.00  1.00
ATOM      7  NL  ALA     1      -1.363   0.265   0.860  1.00  1.00
ATOM      8  HL  ALA     1      -1.914  -0.534   1.016  1.00  1.00
ATOM      9  CA  ALA     1      -0.074   0.012   0.232  1.00  1.00
ATOM     10  HA  ALA     1       0.001  -1.058   0.173  1.00  1.00
ATOM     11  CB  ALA     1      -0.020   0.528  -1.210  1.00  1.00
ATOM     15  CRP ALA     1       1.147   0.408   1.060  1.00  1.00
ATOM     16  OR  ALA     1       1.827  -0.445   1.625  1.00  1.00
ATOM     17  NR  ALA     1       1.461   1.721   1.140  1.00  1.00
ATOM     18  HR  ALA     1       0.821   2.361   0.731  1.00  1.00
ATOM     19  CR  ALA     1       2.614   2.214   1.845  1.00  1.00
END
REMARK X=41 Y=42 
ATOM      1  CL  ALA     1      -3.185   1.487   1.790  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.480   1.139  1.00  1.00
ATOM      6  OL  ALA     1      -1.293   2.532   0.896  1.00  1.00
ATOM      7  NL  ALA     1      -1.349   0.268   0.862  1.00  1.00
ATOM      8  HL  ALA     1      -1.881  -0.527   1.095  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.013   0.226  1.00  1.00
ATOM     10  HA  ALA     1      -0.006  -1.063   0.151  1.00  1.00
ATOM     11  CB  ALA     1      -0.019   0.539  -1.224  1.00  1.00
ATOM     15  CRP ALA     1       1.170   0.398   1.031  1.00  1.00
ATOM     16  OR  ALA     1       1.871  -0.463   1.540  1.00  1.00
ATOM     17  NR  ALA     1       1.447   1.706   1.159  1.00  1.00
ATOM     18  HR  ALA     1       0.788   2.362   0.800  1.00  1.00
ATOM     19  CR  ALA     1       2.602   2.205   1.868  1.00  1.00
END
REMARK X=42 Y=43 
ATOM      1  CL  ALA     1      -3.257   1.605   1.105  1.00  1.00
ATOM      5  CLP ALA     1      -1.941   1.459   0.447  1.00  1.00
ATOM      6  OL  ALA     1      -1.481   2.369  -0.223  1.00  1.00
ATOM      7  NL  ALA     1      -1.303   0.291   0.647  1.00  1.00
ATOM      8  HL  ALA     1      -1.743  -0.379   1.229  1.00  1.00
ATOM      9  CA  ALA     1      -0.011  -0.077   0.099  1.00  1.00
ATOM     10  HA  ALA     1       0.155  -1.099   0.417  1.00  1.00
ATOM     11  CB  ALA     1       0.001  -0.097  -1.439  1.00  1.00
ATOM     15  CRP ALA     1       1.191   0.673   0.683  1.00  1.00
ATOM     16  OR  ALA     1       2.015   0.103   1.375  1.00  1.00
ATOM     17  NR  ALA     1       1.303   1.983   0.393  1.00  1.00
ATOM     18  HR  ALA     1       0.553   2.411  -0.109  1.00  1.00
ATOM     19  CR  ALA     1       2.395   2.811   0.843  1.00  1.00
END
FIXED
  
X: PDB2CONSTANTCreate a constant value from a PDB input file This action is a shortcut and uses the defaults shown here. More details ARGread this single argument from the input rather than the atomic structure=X NOARGS the arguments that are being read from the PDB file are not in the plumed input REFERENCEa file in pdb format containing the reference structure=
regtest/trajectories/path_msd/allv.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/trajectories/path_msd/allv.pdb
    
REMARK X=1 Y=2 
ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00
ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00
ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00
ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00
ATOM      8  HL  ALA     1      -1.845   0.961  -0.011  1.00  1.00
ATOM      9  CA  ALA     1      -0.003  -0.019   0.021  1.00  1.00
ATOM     10  HA  ALA     1       0.205  -1.051   0.259  1.00  1.00
ATOM     11  CB  ALA     1       0.009   0.135  -1.509  1.00  1.00
ATOM     15  CRP ALA     1       1.121   0.799   0.663  1.00  1.00
ATOM     16  OR  ALA     1       1.723   1.669   0.043  1.00  1.00
ATOM     17  NR  ALA     1       1.423   0.519   1.941  1.00  1.00
ATOM     18  HR  ALA     1       0.873  -0.161   2.413  1.00  1.00
ATOM     19  CR  ALA     1       2.477   1.187   2.675  1.00  1.00
END
FIXED
REMARK X=2 Y=3 
ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00
ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00
ATOM      6  OL  ALA     1      -1.201  -0.849   2.425  1.00  1.00
ATOM      7  NL  ALA     1      -1.296   0.337   0.534  1.00  1.00
ATOM      8  HL  ALA     1      -1.807   0.951  -0.044  1.00  1.00
ATOM      9  CA  ALA     1       0.009  -0.067   0.033  1.00  1.00
ATOM     10  HA  ALA     1       0.175  -1.105   0.283  1.00  1.00
ATOM     11  CB  ALA     1       0.027   0.046  -1.501  1.00  1.00
ATOM     15  CRP ALA     1       1.149   0.725   0.654  1.00  1.00
ATOM     16  OR  ALA     1       1.835   1.491  -0.011  1.00  1.00
ATOM     17  NR  ALA     1       1.380   0.537   1.968  1.00  1.00
ATOM     18  HR  ALA     1       0.764  -0.060   2.461  1.00  1.00
ATOM     19  CR  ALA     1       2.431   1.195   2.683  1.00  1.00
END
REMARK X=3 Y=4 
ATOM      1  CL  ALA     1      -2.990   0.383   2.277  1.00  1.00
ATOM      5  CLP ALA     1      -1.664  -0.085   1.831  1.00  1.00
ATOM      6  OL  ALA     1      -0.987  -0.835   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.227   0.364   0.646  1.00  1.00
ATOM      8  HL  ALA     1      -1.798   0.982   0.124  1.00  1.00
ATOM      9  CA  ALA     1       0.026  -0.028   0.044  1.00  1.00
ATOM     10  HA  ALA     1       0.224  -1.060   0.284  1.00  1.00
ATOM     11  CB  ALA     1      -0.076   0.107  -1.483  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.776   0.577  1.00  1.00
ATOM     16  OR  ALA     1       1.900   1.463  -0.158  1.00  1.00
ATOM     17  NR  ALA     1       1.494   0.666   1.888  1.00  1.00
ATOM     18  HR  ALA     1       0.882   0.122   2.437  1.00  1.00
ATOM     19  CR  ALA     1       2.580   1.341   2.529  1.00  1.00
END
REMARK X=4 Y=5 
ATOM      1  CL  ALA     1      -3.006   0.350   2.252  1.00  1.00
ATOM      5  CLP ALA     1      -1.680  -0.112   1.826  1.00  1.00
ATOM      6  OL  ALA     1      -1.025  -0.896   2.508  1.00  1.00
ATOM      7  NL  ALA     1      -1.220   0.368   0.654  1.00  1.00
ATOM      8  HL  ALA     1      -1.771   1.013   0.137  1.00  1.00
ATOM      9  CA  ALA     1       0.040  -0.029   0.062  1.00  1.00
ATOM     10  HA  ALA     1       0.210  -1.076   0.277  1.00  1.00
ATOM     11  CB  ALA     1      -0.066   0.148  -1.465  1.00  1.00
ATOM     15  CRP ALA     1       1.241   0.738   0.605  1.00  1.00
ATOM     16  OR  ALA     1       1.986   1.347  -0.125  1.00  1.00
ATOM     17  NR  ALA     1       1.446   0.694   1.940  1.00  1.00
ATOM     18  HR  ALA     1       0.796   0.210   2.481  1.00  1.00
ATOM     19  CR  ALA     1       2.544   1.350   2.582  1.00  1.00
END
REMARK X=5 Y=6 
ATOM      1  CL  ALA     1      -3.002   0.343   2.271  1.00  1.00
ATOM      5  CLP ALA     1      -1.672  -0.125   1.828  1.00  1.00
ATOM      6  OL  ALA     1      -1.028  -0.942   2.486  1.00  1.00
ATOM      7  NL  ALA     1      -1.213   0.373   0.670  1.00  1.00
ATOM      8  HL  ALA     1      -1.752   1.033   0.169  1.00  1.00
ATOM      9  CA  ALA     1       0.041  -0.032   0.055  1.00  1.00
ATOM     10  HA  ALA     1       0.201  -1.079   0.245  1.00  1.00
ATOM     11  CB  ALA     1      -0.079   0.194  -1.466  1.00  1.00
ATOM     15  CRP ALA     1       1.257   0.720   0.601  1.00  1.00
ATOM     16  OR  ALA     1       2.057   1.240  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.422   0.730   1.942  1.00  1.00
ATOM     18  HR  ALA     1       0.740   0.303   2.500  1.00  1.00
ATOM     19  CR  ALA     1       2.528   1.373   2.598  1.00  1.00
END
REMARK X=6 Y=7 
ATOM      1  CL  ALA     1      -3.144   1.457   1.417  1.00  1.00
ATOM      5  CLP ALA     1      -1.943   0.587   1.450  1.00  1.00
ATOM      6  OL  ALA     1      -1.588   0.028   2.480  1.00  1.00
ATOM      7  NL  ALA     1      -1.281   0.449   0.306  1.00  1.00
ATOM      8  HL  ALA     1      -1.578   0.914  -0.520  1.00  1.00
ATOM      9  CA  ALA     1      -0.132  -0.428   0.139  1.00  1.00
ATOM     10  HA  ALA     1      -0.264  -1.291   0.758  1.00  1.00
ATOM     11  CB  ALA     1      -0.066  -0.855  -1.329  1.00  1.00
ATOM     15  CRP ALA     1       1.193   0.220   0.554  1.00  1.00
ATOM     16  OR  ALA     1       2.195   0.098  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.224   0.872   1.737  1.00  1.00
ATOM     18  HR  ALA     1       0.399   0.943   2.273  1.00  1.00
ATOM     19  CR  ALA     1       2.413   1.511   2.254  1.00  1.00
END
REMARK X=7 Y=8 
ATOM      1  CL  ALA     1      -3.140   1.441   1.453  1.00  1.00
ATOM      5  CLP ALA     1      -1.944   0.576   1.465  1.00  1.00
ATOM      6  OL  ALA     1      -1.587  -0.018   2.487  1.00  1.00
ATOM      7  NL  ALA     1      -1.274   0.465   0.322  1.00  1.00
ATOM      8  HL  ALA     1      -1.571   0.957  -0.486  1.00  1.00
ATOM      9  CA  ALA     1      -0.124  -0.418   0.135  1.00  1.00
ATOM     10  HA  ALA     1      -0.274  -1.304   0.729  1.00  1.00
ATOM     11  CB  ALA     1      -0.063  -0.813  -1.347  1.00  1.00
ATOM     15  CRP ALA     1       1.201   0.199   0.572  1.00  1.00
ATOM     16  OR  ALA     1       2.227   0.007  -0.072  1.00  1.00
ATOM     17  NR  ALA     1       1.215   0.910   1.709  1.00  1.00
ATOM     18  HR  ALA     1       0.369   1.020   2.200  1.00  1.00
ATOM     19  CR  ALA     1       2.393   1.536   2.237  1.00  1.00
END
REMARK X=8 Y=9 
ATOM      1  CL  ALA     1      -3.140   1.420   1.442  1.00  1.00
ATOM      5  CLP ALA     1      -1.948   0.546   1.448  1.00  1.00
ATOM      6  OL  ALA     1      -1.618  -0.065   2.460  1.00  1.00
ATOM      7  NL  ALA     1      -1.255   0.469   0.311  1.00  1.00
ATOM      8  HL  ALA     1      -1.538   0.979  -0.490  1.00  1.00
ATOM      9  CA  ALA     1      -0.107  -0.412   0.124  1.00  1.00
ATOM     10  HA  ALA     1      -0.257  -1.312   0.685  1.00  1.00
ATOM     11  CB  ALA     1      -0.028  -0.770  -1.375  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.186   0.600  1.00  1.00
ATOM     16  OR  ALA     1       2.269  -0.069   0.026  1.00  1.00
ATOM     17  NR  ALA     1       1.193   0.966   1.687  1.00  1.00
ATOM     18  HR  ALA     1       0.333   1.114   2.120  1.00  1.00
ATOM     19  CR  ALA     1       2.377   1.589   2.240  1.00  1.00
END
REMARK X=9 Y=10 
ATOM      1  CL  ALA     1      -3.110   1.698   0.880  1.00  1.00
ATOM      5  CLP ALA     1      -2.021   0.734   1.142  1.00  1.00
ATOM      6  OL  ALA     1      -1.859   0.257   2.258  1.00  1.00
ATOM      7  NL  ALA     1      -1.229   0.414   0.114  1.00  1.00
ATOM      8  HL  ALA     1      -1.371   0.826  -0.771  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.593   0.188  1.00  1.00
ATOM     10  HA  ALA     1      -0.481  -1.374   0.851  1.00  1.00
ATOM     11  CB  ALA     1       0.011  -1.180  -1.220  1.00  1.00
ATOM     15  CRP ALA     1       1.163  -0.060   0.716  1.00  1.00
ATOM     16  OR  ALA     1       2.227  -0.564   0.393  1.00  1.00
ATOM     17  NR  ALA     1       1.127   0.960   1.594  1.00  1.00
ATOM     18  HR  ALA     1       0.234   1.295   1.847  1.00  1.00
ATOM     19  CR  ALA     1       2.303   1.549   2.172  1.00  1.00
END
REMARK X=10 Y=11 
ATOM      1  CL  ALA     1      -3.139   1.652   0.924  1.00  1.00
ATOM      5  CLP ALA     1      -2.039   0.698   1.169  1.00  1.00
ATOM      6  OL  ALA     1      -1.868   0.201   2.278  1.00  1.00
ATOM      7  NL  ALA     1      -1.239   0.411   0.139  1.00  1.00
ATOM      8  HL  ALA     1      -1.385   0.842  -0.737  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.574   0.193  1.00  1.00
ATOM     10  HA  ALA     1      -0.477  -1.381   0.833  1.00  1.00
ATOM     11  CB  ALA     1       0.029  -1.142  -1.231  1.00  1.00
ATOM     15  CRP ALA     1       1.162  -0.048   0.731  1.00  1.00
ATOM     16  OR  ALA     1       2.220  -0.597   0.472  1.00  1.00
ATOM     17  NR  ALA     1       1.122   1.024   1.537  1.00  1.00
ATOM     18  HR  ALA     1       0.233   1.395   1.752  1.00  1.00
ATOM     19  CR  ALA     1       2.300   1.629   2.102  1.00  1.00
END
REMARK X=11 Y=12 
ATOM      1  CL  ALA     1      -3.706   1.088   0.468  1.00  1.00
ATOM      5  CLP ALA     1      -2.458   0.598   1.082  1.00  1.00
ATOM      6  OL  ALA     1      -2.390   0.404   2.277  1.00  1.00
ATOM      7  NL  ALA     1      -1.427   0.382   0.258  1.00  1.00
ATOM      8  HL  ALA     1      -1.513   0.559  -0.713  1.00  1.00
ATOM      9  CA  ALA     1      -0.157  -0.192   0.685  1.00  1.00
ATOM     10  HA  ALA     1      -0.343  -0.912   1.470  1.00  1.00
ATOM     11  CB  ALA     1       0.462  -0.936  -0.512  1.00  1.00
ATOM     15  CRP ALA     1       0.840   0.814   1.241  1.00  1.00
ATOM     16  OR  ALA     1       2.034   0.549   1.354  1.00  1.00
ATOM     17  NR  ALA     1       0.368   2.017   1.650  1.00  1.00
ATOM     18  HR  ALA     1      -0.613   2.169   1.589  1.00  1.00
ATOM     19  CR  ALA     1       1.215   3.044   2.195  1.00  1.00
END
REMARK X=12 Y=13 
ATOM      1  CL  ALA     1      -3.699   1.173   0.487  1.00  1.00
ATOM      5  CLP ALA     1      -2.464   0.631   1.079  1.00  1.00
ATOM      6  OL  ALA     1      -2.402   0.386   2.275  1.00  1.00
ATOM      7  NL  ALA     1      -1.434   0.437   0.260  1.00  1.00
ATOM      8  HL  ALA     1      -1.516   0.652  -0.701  1.00  1.00
ATOM      9  CA  ALA     1      -0.174  -0.174   0.667  1.00  1.00
ATOM     10  HA  ALA     1      -0.377  -0.924   1.411  1.00  1.00
ATOM     11  CB  ALA     1       0.451  -0.859  -0.570  1.00  1.00
ATOM     15  CRP ALA     1       0.839   0.801   1.280  1.00  1.00
ATOM     16  OR  ALA     1       1.999   0.474   1.468  1.00  1.00
ATOM     17  NR  ALA     1       0.404   2.024   1.627  1.00  1.00
ATOM     18  HR  ALA     1      -0.565   2.225   1.505  1.00  1.00
ATOM     19  CR  ALA     1       1.262   3.025   2.214  1.00  1.00
END
REMARK X=13 Y=14 
ATOM      1  CL  ALA     1      -3.653   0.990   1.121  1.00  1.00
ATOM      5  CLP ALA     1      -2.321   0.364   1.249  1.00  1.00
ATOM      6  OL  ALA     1      -2.006  -0.222   2.265  1.00  1.00
ATOM      7  NL  ALA     1      -1.498   0.501   0.205  1.00  1.00
ATOM      8  HL  ALA     1      -1.794   0.978  -0.603  1.00  1.00
ATOM      9  CA  ALA     1      -0.190  -0.127   0.128  1.00  1.00
ATOM     10  HA  ALA     1      -0.216  -1.086   0.627  1.00  1.00
ATOM     11  CB  ALA     1       0.159  -0.359  -1.359  1.00  1.00
ATOM     15  CRP ALA     1       0.933   0.668   0.793  1.00  1.00
ATOM     16  OR  ALA     1       2.107   0.313   0.705  1.00  1.00
ATOM     17  NR  ALA     1       0.604   1.770   1.498  1.00  1.00
ATOM     18  HR  ALA     1      -0.359   1.986   1.593  1.00  1.00
ATOM     19  CR  ALA     1       1.573   2.595   2.158  1.00  1.00
END
REMARK X=14 Y=15 
ATOM      1  CL  ALA     1      -3.641   0.954   1.179  1.00  1.00
ATOM      5  CLP ALA     1      -2.294   0.335   1.290  1.00  1.00
ATOM      6  OL  ALA     1      -1.964  -0.273   2.288  1.00  1.00
ATOM      7  NL  ALA     1      -1.485   0.499   0.235  1.00  1.00
ATOM      8  HL  ALA     1      -1.803   0.995  -0.564  1.00  1.00
ATOM      9  CA  ALA     1      -0.175  -0.118   0.130  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.077   0.601  1.00  1.00
ATOM     11  CB  ALA     1       0.162  -0.300  -1.355  1.00  1.00
ATOM     15  CRP ALA     1       0.952   0.671   0.815  1.00  1.00
ATOM     16  OR  ALA     1       2.104   0.260   0.791  1.00  1.00
ATOM     17  NR  ALA     1       0.633   1.808   1.450  1.00  1.00
ATOM     18  HR  ALA     1      -0.328   2.065   1.503  1.00  1.00
ATOM     19  CR  ALA     1       1.608   2.627   2.129  1.00  1.00
END
REMARK X=15 Y=16 
ATOM      1  CL  ALA     1      -3.635   0.925   1.244  1.00  1.00
ATOM      5  CLP ALA     1      -2.297   0.305   1.309  1.00  1.00
ATOM      6  OL  ALA     1      -1.941  -0.334   2.290  1.00  1.00
ATOM      7  NL  ALA     1      -1.500   0.490   0.251  1.00  1.00
ATOM      8  HL  ALA     1      -1.827   1.009  -0.537  1.00  1.00
ATOM      9  CA  ALA     1      -0.178  -0.110   0.119  1.00  1.00
ATOM     10  HA  ALA     1      -0.205  -1.094   0.536  1.00  1.00
ATOM     11  CB  ALA     1       0.147  -0.217  -1.379  1.00  1.00
ATOM     15  CRP ALA     1       0.943   0.643   0.832  1.00  1.00
ATOM     16  OR  ALA     1       2.074   0.198   0.871  1.00  1.00
ATOM     17  NR  ALA     1       0.637   1.821   1.423  1.00  1.00
ATOM     18  HR  ALA     1      -0.311   2.123   1.418  1.00  1.00
ATOM     19  CR  ALA     1       1.602   2.629   2.109  1.00  1.00
END
REMARK X=16 Y=17 
ATOM      1  CL  ALA     1      -3.632   0.856   1.331  1.00  1.00
ATOM      5  CLP ALA     1      -2.282   0.250   1.355  1.00  1.00
ATOM      6  OL  ALA     1      -1.906  -0.403   2.301  1.00  1.00
ATOM      7  NL  ALA     1      -1.515   0.478   0.275  1.00  1.00
ATOM      8  HL  ALA     1      -1.860   0.990  -0.485  1.00  1.00
ATOM      9  CA  ALA     1      -0.192  -0.105   0.098  1.00  1.00
ATOM     10  HA  ALA     1      -0.204  -1.121   0.473  1.00  1.00
ATOM     11  CB  ALA     1       0.129  -0.136  -1.408  1.00  1.00
ATOM     15  CRP ALA     1       0.931   0.615   0.844  1.00  1.00
ATOM     16  OR  ALA     1       2.043   0.122   0.934  1.00  1.00
ATOM     17  NR  ALA     1       0.651   1.819   1.388  1.00  1.00
ATOM     18  HR  ALA     1      -0.283   2.155   1.349  1.00  1.00
ATOM     19  CR  ALA     1       1.624   2.595   2.115  1.00  1.00
END
REMARK X=17 Y=18 
ATOM      1  CL  ALA     1      -3.628   0.823   1.358  1.00  1.00
ATOM      5  CLP ALA     1      -2.277   0.241   1.370  1.00  1.00
ATOM      6  OL  ALA     1      -1.871  -0.396   2.325  1.00  1.00
ATOM      7  NL  ALA     1      -1.525   0.469   0.284  1.00  1.00
ATOM      8  HL  ALA     1      -1.898   0.970  -0.482  1.00  1.00
ATOM      9  CA  ALA     1      -0.195  -0.094   0.086  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.122   0.423  1.00  1.00
ATOM     11  CB  ALA     1       0.146  -0.058  -1.413  1.00  1.00
ATOM     15  CRP ALA     1       0.919   0.599   0.874  1.00  1.00
ATOM     16  OR  ALA     1       1.997   0.065   1.039  1.00  1.00
ATOM     17  NR  ALA     1       0.655   1.830   1.373  1.00  1.00
ATOM     18  HR  ALA     1      -0.248   2.200   1.261  1.00  1.00
ATOM     19  CR  ALA     1       1.625   2.581   2.124  1.00  1.00
END
REMARK X=18 Y=19 
ATOM      1  CL  ALA     1      -3.539   0.055   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -2.117  -0.208   1.378  1.00  1.00
ATOM      6  OL  ALA     1      -1.453  -0.902   2.125  1.00  1.00
ATOM      7  NL  ALA     1      -1.602   0.351   0.289  1.00  1.00
ATOM      8  HL  ALA     1      -2.185   0.875  -0.310  1.00  1.00
ATOM      9  CA  ALA     1      -0.243   0.129  -0.186  1.00  1.00
ATOM     10  HA  ALA     1      -0.041  -0.924  -0.159  1.00  1.00
ATOM     11  CB  ALA     1      -0.153   0.625  -1.651  1.00  1.00
ATOM     15  CRP ALA     1       0.852   0.806   0.637  1.00  1.00
ATOM     16  OR  ALA     1       2.007   0.400   0.594  1.00  1.00
ATOM     17  NR  ALA     1       0.508   1.855   1.401  1.00  1.00
ATOM     18  HR  ALA     1      -0.445   2.112   1.454  1.00  1.00
ATOM     19  CR  ALA     1       1.460   2.569   2.226  1.00  1.00
END
REMARK X=19 Y=20 
ATOM      1  CL  ALA     1      -3.578   0.084   1.603  1.00  1.00
ATOM      5  CLP ALA     1      -2.140  -0.156   1.375  1.00  1.00
ATOM      6  OL  ALA     1      -1.473  -0.732   2.197  1.00  1.00
ATOM      7  NL  ALA     1      -1.623   0.335   0.237  1.00  1.00
ATOM      8  HL  ALA     1      -2.220   0.753  -0.416  1.00  1.00
ATOM      9  CA  ALA     1      -0.253   0.120  -0.195  1.00  1.00
ATOM     10  HA  ALA     1      -0.048  -0.931  -0.153  1.00  1.00
ATOM     11  CB  ALA     1      -0.128   0.612  -1.663  1.00  1.00
ATOM     15  CRP ALA     1       0.823   0.801   0.637  1.00  1.00
ATOM     16  OR  ALA     1       1.969   0.367   0.665  1.00  1.00
ATOM     17  NR  ALA     1       0.477   1.912   1.333  1.00  1.00
ATOM     18  HR  ALA     1      -0.468   2.199   1.317  1.00  1.00
ATOM     19  CR  ALA     1       1.410   2.627   2.163  1.00  1.00
END
REMARK X=20 Y=21 
ATOM      1  CL  ALA     1      -3.113   1.661   1.504  1.00  1.00
ATOM      5  CLP ALA     1      -1.769   1.059   1.566  1.00  1.00
ATOM      6  OL  ALA     1      -1.201   0.940   2.629  1.00  1.00
ATOM      7  NL  ALA     1      -1.219   0.714   0.392  1.00  1.00
ATOM      8  HL  ALA     1      -1.742   0.797  -0.435  1.00  1.00
ATOM      9  CA  ALA     1       0.058   0.023   0.242  1.00  1.00
ATOM     10  HA  ALA     1      -0.001  -0.896   0.782  1.00  1.00
ATOM     11  CB  ALA     1       0.235  -0.295  -1.249  1.00  1.00
ATOM     15  CRP ALA     1       1.299   0.757   0.745  1.00  1.00
ATOM     16  OR  ALA     1       2.276   0.138   1.135  1.00  1.00
ATOM     17  NR  ALA     1       1.277   2.102   0.736  1.00  1.00
ATOM     18  HR  ALA     1       0.447   2.567   0.458  1.00  1.00
ATOM     19  CR  ALA     1       2.391   2.896   1.191  1.00  1.00
END
REMARK X=21 Y=22 
ATOM      1  CL  ALA     1      -3.089   1.850   1.546  1.00  1.00
ATOM      5  CLP ALA     1      -1.667   1.457   1.629  1.00  1.00
ATOM      6  OL  ALA     1      -0.974   1.868   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.204   0.683   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -1.844   0.360  -0.021  1.00  1.00
ATOM      9  CA  ALA     1       0.126   0.105   0.564  1.00  1.00
ATOM     10  HA  ALA     1       0.239  -0.555   1.391  1.00  1.00
ATOM     11  CB  ALA     1       0.215  -0.722  -0.739  1.00  1.00
ATOM     15  CRP ALA     1       1.311   1.068   0.623  1.00  1.00
ATOM     16  OR  ALA     1       2.369   0.726   1.149  1.00  1.00
ATOM     17  NR  ALA     1       1.156   2.292   0.077  1.00  1.00
ATOM     18  HR  ALA     1       0.273   2.549  -0.285  1.00  1.00
ATOM     19  CR  ALA     1       2.201   3.277   0.107  1.00  1.00
END
REMARK X=22 Y=23 
ATOM      1  CL  ALA     1      -3.102   1.775   1.619  1.00  1.00
ATOM      5  CLP ALA     1      -1.661   1.466   1.659  1.00  1.00
ATOM      6  OL  ALA     1      -0.945   1.961   2.476  1.00  1.00
ATOM      7  NL  ALA     1      -1.205   0.663   0.688  1.00  1.00
ATOM      8  HL  ALA     1      -1.854   0.269   0.091  1.00  1.00
ATOM      9  CA  ALA     1       0.147   0.134   0.561  1.00  1.00
ATOM     10  HA  ALA     1       0.300  -0.545   1.355  1.00  1.00
ATOM     11  CB  ALA     1       0.237  -0.632  -0.776  1.00  1.00
ATOM     15  CRP ALA     1       1.306   1.133   0.628  1.00  1.00
ATOM     16  OR  ALA     1       2.361   0.819   1.176  1.00  1.00
ATOM     17  NR  ALA     1       1.129   2.345   0.068  1.00  1.00
ATOM     18  HR  ALA     1       0.252   2.577  -0.315  1.00  1.00
ATOM     19  CR  ALA     1       2.150   3.364   0.108  1.00  1.00
END
REMARK X=23 Y=24 
ATOM      1  CL  ALA     1      -3.137   1.689   1.564  1.00  1.00
ATOM      5  CLP ALA     1      -1.674   1.466   1.595  1.00  1.00
ATOM      6  OL  ALA     1      -0.991   2.041   2.377  1.00  1.00
ATOM      7  NL  ALA     1      -1.178   0.640   0.664  1.00  1.00
ATOM      8  HL  ALA     1      -1.829   0.190   0.106  1.00  1.00
ATOM      9  CA  ALA     1       0.192   0.170   0.547  1.00  1.00
ATOM     10  HA  ALA     1       0.347  -0.550   1.313  1.00  1.00
ATOM     11  CB  ALA     1       0.333  -0.536  -0.821  1.00  1.00
ATOM     15  CRP ALA     1       1.325   1.194   0.686  1.00  1.00
ATOM     16  OR  ALA     1       2.348   0.906   1.293  1.00  1.00
ATOM     17  NR  ALA     1       1.165   2.398   0.103  1.00  1.00
ATOM     18  HR  ALA     1       0.311   2.617  -0.339  1.00  1.00
ATOM     19  CR  ALA     1       2.173   3.424   0.206  1.00  1.00
END
REMARK X=24 Y=25 
ATOM      1  CL  ALA     1      -3.342   1.726   1.297  1.00  1.00
ATOM      5  CLP ALA     1      -1.882   1.644   1.449  1.00  1.00
ATOM      6  OL  ALA     1      -1.296   2.423   2.124  1.00  1.00
ATOM      7  NL  ALA     1      -1.259   0.684   0.740  1.00  1.00
ATOM      8  HL  ALA     1      -1.839   0.091   0.256  1.00  1.00
ATOM      9  CA  ALA     1       0.138   0.295   0.784  1.00  1.00
ATOM     10  HA  ALA     1       0.267  -0.321   1.638  1.00  1.00
ATOM     11  CB  ALA     1       0.437  -0.541  -0.481  1.00  1.00
ATOM     15  CRP ALA     1       1.207   1.385   0.899  1.00  1.00
ATOM     16  OR  ALA     1       2.160   1.248   1.674  1.00  1.00
ATOM     17  NR  ALA     1       1.092   2.478   0.129  1.00  1.00
ATOM     18  HR  ALA     1       0.291   2.586  -0.440  1.00  1.00
ATOM     19  CR  ALA     1       2.044   3.567   0.190  1.00  1.00
END
REMARK X=25 Y=26 
ATOM      1  CL  ALA     1      -3.361   1.726   1.315  1.00  1.00
ATOM      5  CLP ALA     1      -1.890   1.687   1.423  1.00  1.00
ATOM      6  OL  ALA     1      -1.302   2.522   2.029  1.00  1.00
ATOM      7  NL  ALA     1      -1.285   0.691   0.757  1.00  1.00
ATOM      8  HL  ALA     1      -1.865   0.049   0.326  1.00  1.00
ATOM      9  CA  ALA     1       0.123   0.321   0.749  1.00  1.00
ATOM     10  HA  ALA     1       0.270  -0.331   1.585  1.00  1.00
ATOM     11  CB  ALA     1       0.408  -0.470  -0.534  1.00  1.00
ATOM     15  CRP ALA     1       1.192   1.410   0.900  1.00  1.00
ATOM     16  OR  ALA     1       2.114   1.273   1.701  1.00  1.00
ATOM     17  NR  ALA     1       1.111   2.493   0.112  1.00  1.00
ATOM     18  HR  ALA     1       0.326   2.609  -0.490  1.00  1.00
ATOM     19  CR  ALA     1       2.068   3.578   0.188  1.00  1.00
END
REMARK X=26 Y=27 
ATOM      1  CL  ALA     1      -3.419   1.747   1.251  1.00  1.00
ATOM      5  CLP ALA     1      -1.947   1.630   1.371  1.00  1.00
ATOM      6  OL  ALA     1      -1.331   2.379   2.060  1.00  1.00
ATOM      7  NL  ALA     1      -1.380   0.668   0.616  1.00  1.00
ATOM      8  HL  ALA     1      -1.992   0.115   0.104  1.00  1.00
ATOM      9  CA  ALA     1       0.007   0.227   0.571  1.00  1.00
ATOM     10  HA  ALA     1       0.086  -0.578   1.262  1.00  1.00
ATOM     11  CB  ALA     1       0.288  -0.306  -0.835  1.00  1.00
ATOM     15  CRP ALA     1       1.132   1.190   0.974  1.00  1.00
ATOM     16  OR  ALA     1       1.974   0.858   1.808  1.00  1.00
ATOM     17  NR  ALA     1       1.199   2.390   0.352  1.00  1.00
ATOM     18  HR  ALA     1       0.482   2.643  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.218   3.363   0.657  1.00  1.00
END
REMARK X=27 Y=28 
ATOM      1  CL  ALA     1      -3.430   1.748   1.261  1.00  1.00
ATOM      5  CLP ALA     1      -1.958   1.650   1.340  1.00  1.00
ATOM      6  OL  ALA     1      -1.333   2.471   1.961  1.00  1.00
ATOM      7  NL  ALA     1      -1.392   0.653   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -2.018   0.061   0.177  1.00  1.00
ATOM      9  CA  ALA     1      -0.005   0.219   0.569  1.00  1.00
ATOM     10  HA  ALA     1       0.083  -0.615   1.230  1.00  1.00
ATOM     11  CB  ALA     1       0.266  -0.275  -0.863  1.00  1.00
ATOM     15  CRP ALA     1       1.126   1.166   0.993  1.00  1.00
ATOM     16  OR  ALA     1       1.918   0.834   1.868  1.00  1.00
ATOM     17  NR  ALA     1       1.248   2.346   0.359  1.00  1.00
ATOM     18  HR  ALA     1       0.548   2.609  -0.299  1.00  1.00
ATOM     19  CR  ALA     1       2.271   3.308   0.675  1.00  1.00
END
REMARK X=28 Y=29 
ATOM      1  CL  ALA     1      -3.438   1.702   1.306  1.00  1.00
ATOM      5  CLP ALA     1      -1.962   1.659   1.317  1.00  1.00
ATOM      6  OL  ALA     1      -1.332   2.532   1.870  1.00  1.00
ATOM      7  NL  ALA     1      -1.406   0.632   0.671  1.00  1.00
ATOM      8  HL  ALA     1      -2.029   0.002   0.252  1.00  1.00
ATOM      9  CA  ALA     1      -0.007   0.228   0.554  1.00  1.00
ATOM     10  HA  ALA     1       0.103  -0.631   1.184  1.00  1.00
ATOM     11  CB  ALA     1       0.255  -0.224  -0.899  1.00  1.00
ATOM     15  CRP ALA     1       1.124   1.169   1.002  1.00  1.00
ATOM     16  OR  ALA     1       1.889   0.829   1.901  1.00  1.00
ATOM     17  NR  ALA     1       1.265   2.342   0.365  1.00  1.00
ATOM     18  HR  ALA     1       0.590   2.614  -0.306  1.00  1.00
ATOM     19  CR  ALA     1       2.313   3.280   0.698  1.00  1.00
END
REMARK X=29 Y=30 
ATOM      1  CL  ALA     1      -3.441   1.677   1.342  1.00  1.00
ATOM      5  CLP ALA     1      -1.971   1.666   1.304  1.00  1.00
ATOM      6  OL  ALA     1      -1.348   2.594   1.774  1.00  1.00
ATOM      7  NL  ALA     1      -1.408   0.602   0.696  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.062   0.329  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.235   0.538  1.00  1.00
ATOM     10  HA  ALA     1       0.114  -0.660   1.127  1.00  1.00
ATOM     11  CB  ALA     1       0.223  -0.161  -0.935  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.153   1.020  1.00  1.00
ATOM     16  OR  ALA     1       1.857   0.813   1.931  1.00  1.00
ATOM     17  NR  ALA     1       1.290   2.335   0.385  1.00  1.00
ATOM     18  HR  ALA     1       0.632   2.617  -0.298  1.00  1.00
ATOM     19  CR  ALA     1       2.337   3.252   0.749  1.00  1.00
END
REMARK X=30 Y=31 
ATOM      1  CL  ALA     1      -3.443   1.670   1.352  1.00  1.00
ATOM      5  CLP ALA     1      -1.973   1.670   1.295  1.00  1.00
ATOM      6  OL  ALA     1      -1.351   2.609   1.744  1.00  1.00
ATOM      7  NL  ALA     1      -1.409   0.597   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.076   0.355  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.237   0.533  1.00  1.00
ATOM     10  HA  ALA     1       0.119  -0.663   1.113  1.00  1.00
ATOM     11  CB  ALA     1       0.217  -0.147  -0.945  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.152   1.023  1.00  1.00
ATOM     16  OR  ALA     1       1.849   0.808   1.938  1.00  1.00
ATOM     17  NR  ALA     1       1.296   2.334   0.388  1.00  1.00
ATOM     18  HR  ALA     1       0.638   2.620  -0.293  1.00  1.00
ATOM     19  CR  ALA     1       2.342   3.249   0.754  1.00  1.00
END
REMARK X=31 Y=32 
ATOM      1  CL  ALA     1      -3.451   1.630   1.422  1.00  1.00
ATOM      5  CLP ALA     1      -1.983   1.689   1.248  1.00  1.00
ATOM      6  OL  ALA     1      -1.374   2.689   1.550  1.00  1.00
ATOM      7  NL  ALA     1      -1.421   0.569   0.756  1.00  1.00
ATOM      8  HL  ALA     1      -2.045  -0.151   0.513  1.00  1.00
ATOM      9  CA  ALA     1      -0.017   0.248   0.499  1.00  1.00
ATOM     10  HA  ALA     1       0.149  -0.681   1.023  1.00  1.00
ATOM     11  CB  ALA     1       0.171  -0.057  -0.999  1.00  1.00
ATOM     15  CRP ALA     1       1.111   1.147   1.033  1.00  1.00
ATOM     16  OR  ALA     1       1.807   0.781   1.969  1.00  1.00
ATOM     17  NR  ALA     1       1.327   2.329   0.410  1.00  1.00
ATOM     18  HR  ALA     1       0.679   2.635  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.372   3.237   0.799  1.00  1.00
END
REMARK X=32 Y=33 
ATOM      1  CL  ALA     1      -3.331   1.449   1.617  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.399   1.408  1.00  1.00
ATOM      6  OL  ALA     1      -1.169   2.255   1.904  1.00  1.00
ATOM      7  NL  ALA     1      -1.424   0.371   0.676  1.00  1.00
ATOM      8  HL  ALA     1      -2.118  -0.203   0.289  1.00  1.00
ATOM      9  CA  ALA     1      -0.062   0.001   0.310  1.00  1.00
ATOM     10  HA  ALA     1      -0.008  -1.054   0.497  1.00  1.00
ATOM     11  CB  ALA     1       0.131   0.162  -1.216  1.00  1.00
ATOM     15  CRP ALA     1       1.142   0.546   1.099  1.00  1.00
ATOM     16  OR  ALA     1       1.741  -0.171   1.894  1.00  1.00
ATOM     17  NR  ALA     1       1.537   1.815   0.864  1.00  1.00
ATOM     18  HR  ALA     1       0.963   2.391   0.297  1.00  1.00
ATOM     19  CR  ALA     1       2.669   2.426   1.513  1.00  1.00
END
REMARK X=33 Y=34 
ATOM      1  CL  ALA     1      -3.321   1.436   1.650  1.00  1.00
ATOM      5  CLP ALA     1      -1.870   1.422   1.372  1.00  1.00
ATOM      6  OL  ALA     1      -1.182   2.323   1.789  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.347   0.697  1.00  1.00
ATOM      8  HL  ALA     1      -2.106  -0.263   0.374  1.00  1.00
ATOM      9  CA  ALA     1      -0.057   0.008   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.002  -1.051   0.446  1.00  1.00
ATOM     11  CB  ALA     1       0.113   0.213  -1.212  1.00  1.00
ATOM     15  CRP ALA     1       1.139   0.538   1.102  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.196   1.881  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.803   0.879  1.00  1.00
ATOM     18  HR  ALA     1       0.972   2.397   0.326  1.00  1.00
ATOM     19  CR  ALA     1       2.672   2.407   1.539  1.00  1.00
END
REMARK X=34 Y=35 
ATOM      1  CL  ALA     1      -3.318   1.434   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -1.871   1.426   1.363  1.00  1.00
ATOM      6  OL  ALA     1      -1.186   2.341   1.756  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.343   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.101  -0.279   0.398  1.00  1.00
ATOM      9  CA  ALA     1      -0.058   0.010   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.005  -1.051   0.433  1.00  1.00
ATOM     11  CB  ALA     1       0.109   0.227  -1.215  1.00  1.00
ATOM     15  CRP ALA     1       1.138   0.536   1.100  1.00  1.00
ATOM     16  OR  ALA     1       1.723  -0.202   1.878  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.802   0.887  1.00  1.00
ATOM     18  HR  ALA     1       0.970   2.398   0.335  1.00  1.00
ATOM     19  CR  ALA     1       2.675   2.402   1.547  1.00  1.00
END
REMARK X=35 Y=36 
ATOM      1  CL  ALA     1      -3.297   1.417   1.700  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.437   1.310  1.00  1.00
ATOM      6  OL  ALA     1      -1.214   2.432   1.560  1.00  1.00
ATOM      7  NL  ALA     1      -1.412   0.320   0.746  1.00  1.00
ATOM      8  HL  ALA     1      -2.060  -0.372   0.544  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.025   0.282  1.00  1.00
ATOM     10  HA  ALA     1       0.023  -1.051   0.357  1.00  1.00
ATOM     11  CB  ALA     1       0.071   0.308  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.141   0.510   1.103  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.245   1.863  1.00  1.00
ATOM     17  NR  ALA     1       1.541   1.794   0.938  1.00  1.00
ATOM     18  HR  ALA     1       0.957   2.397   0.401  1.00  1.00
ATOM     19  CR  ALA     1       2.683   2.371   1.604  1.00  1.00
END
REMARK X=36 Y=37 
ATOM      1  CL  ALA     1      -3.283   1.421   1.730  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.449   1.277  1.00  1.00
ATOM      6  OL  ALA     1      -1.222   2.476   1.436  1.00  1.00
ATOM      7  NL  ALA     1      -1.405   0.299   0.773  1.00  1.00
ATOM      8  HL  ALA     1      -2.034  -0.422   0.640  1.00  1.00
ATOM      9  CA  ALA     1      -0.063   0.028   0.272  1.00  1.00
ATOM     10  HA  ALA     1       0.015  -1.050   0.307  1.00  1.00
ATOM     11  CB  ALA     1       0.057   0.364  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.134   0.492   1.093  1.00  1.00
ATOM     16  OR  ALA     1       1.729  -0.288   1.825  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.779   0.976  1.00  1.00
ATOM     18  HR  ALA     1       0.945   2.388   0.456  1.00  1.00
ATOM     19  CR  ALA     1       2.682   2.335   1.653  1.00  1.00
END
REMARK X=37 Y=38 
ATOM      1  CL  ALA     1      -3.265   1.435   1.760  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.457   1.257  1.00  1.00
ATOM      6  OL  ALA     1      -1.229   2.500   1.343  1.00  1.00
ATOM      7  NL  ALA     1      -1.398   0.292   0.802  1.00  1.00
ATOM      8  HL  ALA     1      -2.014  -0.454   0.728  1.00  1.00
ATOM      9  CA  ALA     1      -0.067   0.024   0.264  1.00  1.00
ATOM     10  HA  ALA     1       0.011  -1.049   0.257  1.00  1.00
ATOM     11  CB  ALA     1       0.028   0.426  -1.206  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.464   1.092  1.00  1.00
ATOM     16  OR  ALA     1       1.748  -0.346   1.781  1.00  1.00
ATOM     17  NR  ALA     1       1.532   1.754   1.029  1.00  1.00
ATOM     18  HR  ALA     1       0.931   2.385   0.536  1.00  1.00
ATOM     19  CR  ALA     1       2.676   2.280   1.721  1.00  1.00
END
REMARK X=38 Y=39 
ATOM      1  CL  ALA     1      -3.236   1.453   1.772  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.473   1.217  1.00  1.00
ATOM      6  OL  ALA     1      -1.244   2.522   1.222  1.00  1.00
ATOM      7  NL  ALA     1      -1.388   0.292   0.824  1.00  1.00
ATOM      8  HL  ALA     1      -1.982  -0.485   0.827  1.00  1.00
ATOM      9  CA  ALA     1      -0.066   0.031   0.248  1.00  1.00
ATOM     10  HA  ALA     1       0.018  -1.048   0.230  1.00  1.00
ATOM     11  CB  ALA     1       0.011   0.464  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.452   1.088  1.00  1.00
ATOM     16  OR  ALA     1       1.767  -0.373   1.737  1.00  1.00
ATOM     17  NR  ALA     1       1.517   1.749   1.061  1.00  1.00
ATOM     18  HR  ALA     1       0.906   2.387   0.586  1.00  1.00
ATOM     19  CR  ALA     1       2.660   2.262   1.754  1.00  1.00
END
REMARK X=39 Y=40 
ATOM      1  CL  ALA     1      -3.225   1.461   1.784  1.00  1.00
ATOM      5  CLP ALA     1      -1.878   1.466   1.191  1.00  1.00
ATOM      6  OL  ALA     1      -1.276   2.527   1.106  1.00  1.00
ATOM      7  NL  ALA     1      -1.375   0.274   0.839  1.00  1.00
ATOM      8  HL  ALA     1      -1.947  -0.517   0.921  1.00  1.00
ATOM      9  CA  ALA     1      -0.077   0.024   0.236  1.00  1.00
ATOM     10  HA  ALA     1       0.009  -1.048   0.194  1.00  1.00
ATOM     11  CB  ALA     1      -0.004   0.503  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.436   1.066  1.00  1.00
ATOM     16  OR  ALA     1       1.800  -0.403   1.678  1.00  1.00
ATOM     17  NR  ALA     1       1.483   1.736   1.091  1.00  1.00
ATOM     18  HR  ALA     1       0.861   2.388   0.647  1.00  1.00
ATOM     19  CR  ALA     1       2.642   2.246   1.792  1.00  1.00
END
REMARK X=40 Y=41 
ATOM      1  CL  ALA     1      -3.212   1.465   1.797  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.470   1.168  1.00  1.00
ATOM      6  OL  ALA     1      -1.286   2.526   1.008  1.00  1.00
ATOM      7  NL  ALA     1      -1.363   0.265   0.860  1.00  1.00
ATOM      8  HL  ALA     1      -1.914  -0.534   1.016  1.00  1.00
ATOM      9  CA  ALA     1      -0.074   0.012   0.232  1.00  1.00
ATOM     10  HA  ALA     1       0.001  -1.058   0.173  1.00  1.00
ATOM     11  CB  ALA     1      -0.020   0.528  -1.210  1.00  1.00
ATOM     15  CRP ALA     1       1.147   0.408   1.060  1.00  1.00
ATOM     16  OR  ALA     1       1.827  -0.445   1.625  1.00  1.00
ATOM     17  NR  ALA     1       1.461   1.721   1.140  1.00  1.00
ATOM     18  HR  ALA     1       0.821   2.361   0.731  1.00  1.00
ATOM     19  CR  ALA     1       2.614   2.214   1.845  1.00  1.00
END
REMARK X=41 Y=42 
ATOM      1  CL  ALA     1      -3.185   1.487   1.790  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.480   1.139  1.00  1.00
ATOM      6  OL  ALA     1      -1.293   2.532   0.896  1.00  1.00
ATOM      7  NL  ALA     1      -1.349   0.268   0.862  1.00  1.00
ATOM      8  HL  ALA     1      -1.881  -0.527   1.095  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.013   0.226  1.00  1.00
ATOM     10  HA  ALA     1      -0.006  -1.063   0.151  1.00  1.00
ATOM     11  CB  ALA     1      -0.019   0.539  -1.224  1.00  1.00
ATOM     15  CRP ALA     1       1.170   0.398   1.031  1.00  1.00
ATOM     16  OR  ALA     1       1.871  -0.463   1.540  1.00  1.00
ATOM     17  NR  ALA     1       1.447   1.706   1.159  1.00  1.00
ATOM     18  HR  ALA     1       0.788   2.362   0.800  1.00  1.00
ATOM     19  CR  ALA     1       2.602   2.205   1.868  1.00  1.00
END
REMARK X=42 Y=43 
ATOM      1  CL  ALA     1      -3.257   1.605   1.105  1.00  1.00
ATOM      5  CLP ALA     1      -1.941   1.459   0.447  1.00  1.00
ATOM      6  OL  ALA     1      -1.481   2.369  -0.223  1.00  1.00
ATOM      7  NL  ALA     1      -1.303   0.291   0.647  1.00  1.00
ATOM      8  HL  ALA     1      -1.743  -0.379   1.229  1.00  1.00
ATOM      9  CA  ALA     1      -0.011  -0.077   0.099  1.00  1.00
ATOM     10  HA  ALA     1       0.155  -1.099   0.417  1.00  1.00
ATOM     11  CB  ALA     1       0.001  -0.097  -1.439  1.00  1.00
ATOM     15  CRP ALA     1       1.191   0.673   0.683  1.00  1.00
ATOM     16  OR  ALA     1       2.015   0.103   1.375  1.00  1.00
ATOM     17  NR  ALA     1       1.303   1.983   0.393  1.00  1.00
ATOM     18  HR  ALA     1       0.553   2.411  -0.109  1.00  1.00
ATOM     19  CR  ALA     1       2.395   2.811   0.843  1.00  1.00
END
FIXED
  
  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
# PLUMED interprets the command:
# X: PDB2CONSTANT ARG=X NOARGS REFERENCE=regtest/trajectories/path_msd/allv.pdb
# as follows (Click the red comment above to revert to the short version of the input):
XThe CONSTANT action with label X calculates the following quantities:
 Quantity   
 Type   
 Description  
X
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42
# --- End of included input --- YThe PDB2CONSTANT action with label Y calculates the following quantities:
 Quantity   
 Type   
 Description  
Y
vector
a value that is constructed from the information in the PDB file: PDB2CONSTANTCreate a constant value from a PDB input file This action is a shortcut and it has hidden defaults. More details ARGread this single argument from the input rather than the atomic structure=Y NOARGS the arguments that are being read from the PDB file are not in the plumed input REFERENCEa file in pdb format containing the reference structure=
regtest/trajectories/path_msd/allv.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/trajectories/path_msd/allv.pdb
    
REMARK X=1 Y=2 
ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00
ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00
ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00
ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00
ATOM      8  HL  ALA     1      -1.845   0.961  -0.011  1.00  1.00
ATOM      9  CA  ALA     1      -0.003  -0.019   0.021  1.00  1.00
ATOM     10  HA  ALA     1       0.205  -1.051   0.259  1.00  1.00
ATOM     11  CB  ALA     1       0.009   0.135  -1.509  1.00  1.00
ATOM     15  CRP ALA     1       1.121   0.799   0.663  1.00  1.00
ATOM     16  OR  ALA     1       1.723   1.669   0.043  1.00  1.00
ATOM     17  NR  ALA     1       1.423   0.519   1.941  1.00  1.00
ATOM     18  HR  ALA     1       0.873  -0.161   2.413  1.00  1.00
ATOM     19  CR  ALA     1       2.477   1.187   2.675  1.00  1.00
END
FIXED
REMARK X=2 Y=3 
ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00
ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00
ATOM      6  OL  ALA     1      -1.201  -0.849   2.425  1.00  1.00
ATOM      7  NL  ALA     1      -1.296   0.337   0.534  1.00  1.00
ATOM      8  HL  ALA     1      -1.807   0.951  -0.044  1.00  1.00
ATOM      9  CA  ALA     1       0.009  -0.067   0.033  1.00  1.00
ATOM     10  HA  ALA     1       0.175  -1.105   0.283  1.00  1.00
ATOM     11  CB  ALA     1       0.027   0.046  -1.501  1.00  1.00
ATOM     15  CRP ALA     1       1.149   0.725   0.654  1.00  1.00
ATOM     16  OR  ALA     1       1.835   1.491  -0.011  1.00  1.00
ATOM     17  NR  ALA     1       1.380   0.537   1.968  1.00  1.00
ATOM     18  HR  ALA     1       0.764  -0.060   2.461  1.00  1.00
ATOM     19  CR  ALA     1       2.431   1.195   2.683  1.00  1.00
END
REMARK X=3 Y=4 
ATOM      1  CL  ALA     1      -2.990   0.383   2.277  1.00  1.00
ATOM      5  CLP ALA     1      -1.664  -0.085   1.831  1.00  1.00
ATOM      6  OL  ALA     1      -0.987  -0.835   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.227   0.364   0.646  1.00  1.00
ATOM      8  HL  ALA     1      -1.798   0.982   0.124  1.00  1.00
ATOM      9  CA  ALA     1       0.026  -0.028   0.044  1.00  1.00
ATOM     10  HA  ALA     1       0.224  -1.060   0.284  1.00  1.00
ATOM     11  CB  ALA     1      -0.076   0.107  -1.483  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.776   0.577  1.00  1.00
ATOM     16  OR  ALA     1       1.900   1.463  -0.158  1.00  1.00
ATOM     17  NR  ALA     1       1.494   0.666   1.888  1.00  1.00
ATOM     18  HR  ALA     1       0.882   0.122   2.437  1.00  1.00
ATOM     19  CR  ALA     1       2.580   1.341   2.529  1.00  1.00
END
REMARK X=4 Y=5 
ATOM      1  CL  ALA     1      -3.006   0.350   2.252  1.00  1.00
ATOM      5  CLP ALA     1      -1.680  -0.112   1.826  1.00  1.00
ATOM      6  OL  ALA     1      -1.025  -0.896   2.508  1.00  1.00
ATOM      7  NL  ALA     1      -1.220   0.368   0.654  1.00  1.00
ATOM      8  HL  ALA     1      -1.771   1.013   0.137  1.00  1.00
ATOM      9  CA  ALA     1       0.040  -0.029   0.062  1.00  1.00
ATOM     10  HA  ALA     1       0.210  -1.076   0.277  1.00  1.00
ATOM     11  CB  ALA     1      -0.066   0.148  -1.465  1.00  1.00
ATOM     15  CRP ALA     1       1.241   0.738   0.605  1.00  1.00
ATOM     16  OR  ALA     1       1.986   1.347  -0.125  1.00  1.00
ATOM     17  NR  ALA     1       1.446   0.694   1.940  1.00  1.00
ATOM     18  HR  ALA     1       0.796   0.210   2.481  1.00  1.00
ATOM     19  CR  ALA     1       2.544   1.350   2.582  1.00  1.00
END
REMARK X=5 Y=6 
ATOM      1  CL  ALA     1      -3.002   0.343   2.271  1.00  1.00
ATOM      5  CLP ALA     1      -1.672  -0.125   1.828  1.00  1.00
ATOM      6  OL  ALA     1      -1.028  -0.942   2.486  1.00  1.00
ATOM      7  NL  ALA     1      -1.213   0.373   0.670  1.00  1.00
ATOM      8  HL  ALA     1      -1.752   1.033   0.169  1.00  1.00
ATOM      9  CA  ALA     1       0.041  -0.032   0.055  1.00  1.00
ATOM     10  HA  ALA     1       0.201  -1.079   0.245  1.00  1.00
ATOM     11  CB  ALA     1      -0.079   0.194  -1.466  1.00  1.00
ATOM     15  CRP ALA     1       1.257   0.720   0.601  1.00  1.00
ATOM     16  OR  ALA     1       2.057   1.240  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.422   0.730   1.942  1.00  1.00
ATOM     18  HR  ALA     1       0.740   0.303   2.500  1.00  1.00
ATOM     19  CR  ALA     1       2.528   1.373   2.598  1.00  1.00
END
REMARK X=6 Y=7 
ATOM      1  CL  ALA     1      -3.144   1.457   1.417  1.00  1.00
ATOM      5  CLP ALA     1      -1.943   0.587   1.450  1.00  1.00
ATOM      6  OL  ALA     1      -1.588   0.028   2.480  1.00  1.00
ATOM      7  NL  ALA     1      -1.281   0.449   0.306  1.00  1.00
ATOM      8  HL  ALA     1      -1.578   0.914  -0.520  1.00  1.00
ATOM      9  CA  ALA     1      -0.132  -0.428   0.139  1.00  1.00
ATOM     10  HA  ALA     1      -0.264  -1.291   0.758  1.00  1.00
ATOM     11  CB  ALA     1      -0.066  -0.855  -1.329  1.00  1.00
ATOM     15  CRP ALA     1       1.193   0.220   0.554  1.00  1.00
ATOM     16  OR  ALA     1       2.195   0.098  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.224   0.872   1.737  1.00  1.00
ATOM     18  HR  ALA     1       0.399   0.943   2.273  1.00  1.00
ATOM     19  CR  ALA     1       2.413   1.511   2.254  1.00  1.00
END
REMARK X=7 Y=8 
ATOM      1  CL  ALA     1      -3.140   1.441   1.453  1.00  1.00
ATOM      5  CLP ALA     1      -1.944   0.576   1.465  1.00  1.00
ATOM      6  OL  ALA     1      -1.587  -0.018   2.487  1.00  1.00
ATOM      7  NL  ALA     1      -1.274   0.465   0.322  1.00  1.00
ATOM      8  HL  ALA     1      -1.571   0.957  -0.486  1.00  1.00
ATOM      9  CA  ALA     1      -0.124  -0.418   0.135  1.00  1.00
ATOM     10  HA  ALA     1      -0.274  -1.304   0.729  1.00  1.00
ATOM     11  CB  ALA     1      -0.063  -0.813  -1.347  1.00  1.00
ATOM     15  CRP ALA     1       1.201   0.199   0.572  1.00  1.00
ATOM     16  OR  ALA     1       2.227   0.007  -0.072  1.00  1.00
ATOM     17  NR  ALA     1       1.215   0.910   1.709  1.00  1.00
ATOM     18  HR  ALA     1       0.369   1.020   2.200  1.00  1.00
ATOM     19  CR  ALA     1       2.393   1.536   2.237  1.00  1.00
END
REMARK X=8 Y=9 
ATOM      1  CL  ALA     1      -3.140   1.420   1.442  1.00  1.00
ATOM      5  CLP ALA     1      -1.948   0.546   1.448  1.00  1.00
ATOM      6  OL  ALA     1      -1.618  -0.065   2.460  1.00  1.00
ATOM      7  NL  ALA     1      -1.255   0.469   0.311  1.00  1.00
ATOM      8  HL  ALA     1      -1.538   0.979  -0.490  1.00  1.00
ATOM      9  CA  ALA     1      -0.107  -0.412   0.124  1.00  1.00
ATOM     10  HA  ALA     1      -0.257  -1.312   0.685  1.00  1.00
ATOM     11  CB  ALA     1      -0.028  -0.770  -1.375  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.186   0.600  1.00  1.00
ATOM     16  OR  ALA     1       2.269  -0.069   0.026  1.00  1.00
ATOM     17  NR  ALA     1       1.193   0.966   1.687  1.00  1.00
ATOM     18  HR  ALA     1       0.333   1.114   2.120  1.00  1.00
ATOM     19  CR  ALA     1       2.377   1.589   2.240  1.00  1.00
END
REMARK X=9 Y=10 
ATOM      1  CL  ALA     1      -3.110   1.698   0.880  1.00  1.00
ATOM      5  CLP ALA     1      -2.021   0.734   1.142  1.00  1.00
ATOM      6  OL  ALA     1      -1.859   0.257   2.258  1.00  1.00
ATOM      7  NL  ALA     1      -1.229   0.414   0.114  1.00  1.00
ATOM      8  HL  ALA     1      -1.371   0.826  -0.771  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.593   0.188  1.00  1.00
ATOM     10  HA  ALA     1      -0.481  -1.374   0.851  1.00  1.00
ATOM     11  CB  ALA     1       0.011  -1.180  -1.220  1.00  1.00
ATOM     15  CRP ALA     1       1.163  -0.060   0.716  1.00  1.00
ATOM     16  OR  ALA     1       2.227  -0.564   0.393  1.00  1.00
ATOM     17  NR  ALA     1       1.127   0.960   1.594  1.00  1.00
ATOM     18  HR  ALA     1       0.234   1.295   1.847  1.00  1.00
ATOM     19  CR  ALA     1       2.303   1.549   2.172  1.00  1.00
END
REMARK X=10 Y=11 
ATOM      1  CL  ALA     1      -3.139   1.652   0.924  1.00  1.00
ATOM      5  CLP ALA     1      -2.039   0.698   1.169  1.00  1.00
ATOM      6  OL  ALA     1      -1.868   0.201   2.278  1.00  1.00
ATOM      7  NL  ALA     1      -1.239   0.411   0.139  1.00  1.00
ATOM      8  HL  ALA     1      -1.385   0.842  -0.737  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.574   0.193  1.00  1.00
ATOM     10  HA  ALA     1      -0.477  -1.381   0.833  1.00  1.00
ATOM     11  CB  ALA     1       0.029  -1.142  -1.231  1.00  1.00
ATOM     15  CRP ALA     1       1.162  -0.048   0.731  1.00  1.00
ATOM     16  OR  ALA     1       2.220  -0.597   0.472  1.00  1.00
ATOM     17  NR  ALA     1       1.122   1.024   1.537  1.00  1.00
ATOM     18  HR  ALA     1       0.233   1.395   1.752  1.00  1.00
ATOM     19  CR  ALA     1       2.300   1.629   2.102  1.00  1.00
END
REMARK X=11 Y=12 
ATOM      1  CL  ALA     1      -3.706   1.088   0.468  1.00  1.00
ATOM      5  CLP ALA     1      -2.458   0.598   1.082  1.00  1.00
ATOM      6  OL  ALA     1      -2.390   0.404   2.277  1.00  1.00
ATOM      7  NL  ALA     1      -1.427   0.382   0.258  1.00  1.00
ATOM      8  HL  ALA     1      -1.513   0.559  -0.713  1.00  1.00
ATOM      9  CA  ALA     1      -0.157  -0.192   0.685  1.00  1.00
ATOM     10  HA  ALA     1      -0.343  -0.912   1.470  1.00  1.00
ATOM     11  CB  ALA     1       0.462  -0.936  -0.512  1.00  1.00
ATOM     15  CRP ALA     1       0.840   0.814   1.241  1.00  1.00
ATOM     16  OR  ALA     1       2.034   0.549   1.354  1.00  1.00
ATOM     17  NR  ALA     1       0.368   2.017   1.650  1.00  1.00
ATOM     18  HR  ALA     1      -0.613   2.169   1.589  1.00  1.00
ATOM     19  CR  ALA     1       1.215   3.044   2.195  1.00  1.00
END
REMARK X=12 Y=13 
ATOM      1  CL  ALA     1      -3.699   1.173   0.487  1.00  1.00
ATOM      5  CLP ALA     1      -2.464   0.631   1.079  1.00  1.00
ATOM      6  OL  ALA     1      -2.402   0.386   2.275  1.00  1.00
ATOM      7  NL  ALA     1      -1.434   0.437   0.260  1.00  1.00
ATOM      8  HL  ALA     1      -1.516   0.652  -0.701  1.00  1.00
ATOM      9  CA  ALA     1      -0.174  -0.174   0.667  1.00  1.00
ATOM     10  HA  ALA     1      -0.377  -0.924   1.411  1.00  1.00
ATOM     11  CB  ALA     1       0.451  -0.859  -0.570  1.00  1.00
ATOM     15  CRP ALA     1       0.839   0.801   1.280  1.00  1.00
ATOM     16  OR  ALA     1       1.999   0.474   1.468  1.00  1.00
ATOM     17  NR  ALA     1       0.404   2.024   1.627  1.00  1.00
ATOM     18  HR  ALA     1      -0.565   2.225   1.505  1.00  1.00
ATOM     19  CR  ALA     1       1.262   3.025   2.214  1.00  1.00
END
REMARK X=13 Y=14 
ATOM      1  CL  ALA     1      -3.653   0.990   1.121  1.00  1.00
ATOM      5  CLP ALA     1      -2.321   0.364   1.249  1.00  1.00
ATOM      6  OL  ALA     1      -2.006  -0.222   2.265  1.00  1.00
ATOM      7  NL  ALA     1      -1.498   0.501   0.205  1.00  1.00
ATOM      8  HL  ALA     1      -1.794   0.978  -0.603  1.00  1.00
ATOM      9  CA  ALA     1      -0.190  -0.127   0.128  1.00  1.00
ATOM     10  HA  ALA     1      -0.216  -1.086   0.627  1.00  1.00
ATOM     11  CB  ALA     1       0.159  -0.359  -1.359  1.00  1.00
ATOM     15  CRP ALA     1       0.933   0.668   0.793  1.00  1.00
ATOM     16  OR  ALA     1       2.107   0.313   0.705  1.00  1.00
ATOM     17  NR  ALA     1       0.604   1.770   1.498  1.00  1.00
ATOM     18  HR  ALA     1      -0.359   1.986   1.593  1.00  1.00
ATOM     19  CR  ALA     1       1.573   2.595   2.158  1.00  1.00
END
REMARK X=14 Y=15 
ATOM      1  CL  ALA     1      -3.641   0.954   1.179  1.00  1.00
ATOM      5  CLP ALA     1      -2.294   0.335   1.290  1.00  1.00
ATOM      6  OL  ALA     1      -1.964  -0.273   2.288  1.00  1.00
ATOM      7  NL  ALA     1      -1.485   0.499   0.235  1.00  1.00
ATOM      8  HL  ALA     1      -1.803   0.995  -0.564  1.00  1.00
ATOM      9  CA  ALA     1      -0.175  -0.118   0.130  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.077   0.601  1.00  1.00
ATOM     11  CB  ALA     1       0.162  -0.300  -1.355  1.00  1.00
ATOM     15  CRP ALA     1       0.952   0.671   0.815  1.00  1.00
ATOM     16  OR  ALA     1       2.104   0.260   0.791  1.00  1.00
ATOM     17  NR  ALA     1       0.633   1.808   1.450  1.00  1.00
ATOM     18  HR  ALA     1      -0.328   2.065   1.503  1.00  1.00
ATOM     19  CR  ALA     1       1.608   2.627   2.129  1.00  1.00
END
REMARK X=15 Y=16 
ATOM      1  CL  ALA     1      -3.635   0.925   1.244  1.00  1.00
ATOM      5  CLP ALA     1      -2.297   0.305   1.309  1.00  1.00
ATOM      6  OL  ALA     1      -1.941  -0.334   2.290  1.00  1.00
ATOM      7  NL  ALA     1      -1.500   0.490   0.251  1.00  1.00
ATOM      8  HL  ALA     1      -1.827   1.009  -0.537  1.00  1.00
ATOM      9  CA  ALA     1      -0.178  -0.110   0.119  1.00  1.00
ATOM     10  HA  ALA     1      -0.205  -1.094   0.536  1.00  1.00
ATOM     11  CB  ALA     1       0.147  -0.217  -1.379  1.00  1.00
ATOM     15  CRP ALA     1       0.943   0.643   0.832  1.00  1.00
ATOM     16  OR  ALA     1       2.074   0.198   0.871  1.00  1.00
ATOM     17  NR  ALA     1       0.637   1.821   1.423  1.00  1.00
ATOM     18  HR  ALA     1      -0.311   2.123   1.418  1.00  1.00
ATOM     19  CR  ALA     1       1.602   2.629   2.109  1.00  1.00
END
REMARK X=16 Y=17 
ATOM      1  CL  ALA     1      -3.632   0.856   1.331  1.00  1.00
ATOM      5  CLP ALA     1      -2.282   0.250   1.355  1.00  1.00
ATOM      6  OL  ALA     1      -1.906  -0.403   2.301  1.00  1.00
ATOM      7  NL  ALA     1      -1.515   0.478   0.275  1.00  1.00
ATOM      8  HL  ALA     1      -1.860   0.990  -0.485  1.00  1.00
ATOM      9  CA  ALA     1      -0.192  -0.105   0.098  1.00  1.00
ATOM     10  HA  ALA     1      -0.204  -1.121   0.473  1.00  1.00
ATOM     11  CB  ALA     1       0.129  -0.136  -1.408  1.00  1.00
ATOM     15  CRP ALA     1       0.931   0.615   0.844  1.00  1.00
ATOM     16  OR  ALA     1       2.043   0.122   0.934  1.00  1.00
ATOM     17  NR  ALA     1       0.651   1.819   1.388  1.00  1.00
ATOM     18  HR  ALA     1      -0.283   2.155   1.349  1.00  1.00
ATOM     19  CR  ALA     1       1.624   2.595   2.115  1.00  1.00
END
REMARK X=17 Y=18 
ATOM      1  CL  ALA     1      -3.628   0.823   1.358  1.00  1.00
ATOM      5  CLP ALA     1      -2.277   0.241   1.370  1.00  1.00
ATOM      6  OL  ALA     1      -1.871  -0.396   2.325  1.00  1.00
ATOM      7  NL  ALA     1      -1.525   0.469   0.284  1.00  1.00
ATOM      8  HL  ALA     1      -1.898   0.970  -0.482  1.00  1.00
ATOM      9  CA  ALA     1      -0.195  -0.094   0.086  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.122   0.423  1.00  1.00
ATOM     11  CB  ALA     1       0.146  -0.058  -1.413  1.00  1.00
ATOM     15  CRP ALA     1       0.919   0.599   0.874  1.00  1.00
ATOM     16  OR  ALA     1       1.997   0.065   1.039  1.00  1.00
ATOM     17  NR  ALA     1       0.655   1.830   1.373  1.00  1.00
ATOM     18  HR  ALA     1      -0.248   2.200   1.261  1.00  1.00
ATOM     19  CR  ALA     1       1.625   2.581   2.124  1.00  1.00
END
REMARK X=18 Y=19 
ATOM      1  CL  ALA     1      -3.539   0.055   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -2.117  -0.208   1.378  1.00  1.00
ATOM      6  OL  ALA     1      -1.453  -0.902   2.125  1.00  1.00
ATOM      7  NL  ALA     1      -1.602   0.351   0.289  1.00  1.00
ATOM      8  HL  ALA     1      -2.185   0.875  -0.310  1.00  1.00
ATOM      9  CA  ALA     1      -0.243   0.129  -0.186  1.00  1.00
ATOM     10  HA  ALA     1      -0.041  -0.924  -0.159  1.00  1.00
ATOM     11  CB  ALA     1      -0.153   0.625  -1.651  1.00  1.00
ATOM     15  CRP ALA     1       0.852   0.806   0.637  1.00  1.00
ATOM     16  OR  ALA     1       2.007   0.400   0.594  1.00  1.00
ATOM     17  NR  ALA     1       0.508   1.855   1.401  1.00  1.00
ATOM     18  HR  ALA     1      -0.445   2.112   1.454  1.00  1.00
ATOM     19  CR  ALA     1       1.460   2.569   2.226  1.00  1.00
END
REMARK X=19 Y=20 
ATOM      1  CL  ALA     1      -3.578   0.084   1.603  1.00  1.00
ATOM      5  CLP ALA     1      -2.140  -0.156   1.375  1.00  1.00
ATOM      6  OL  ALA     1      -1.473  -0.732   2.197  1.00  1.00
ATOM      7  NL  ALA     1      -1.623   0.335   0.237  1.00  1.00
ATOM      8  HL  ALA     1      -2.220   0.753  -0.416  1.00  1.00
ATOM      9  CA  ALA     1      -0.253   0.120  -0.195  1.00  1.00
ATOM     10  HA  ALA     1      -0.048  -0.931  -0.153  1.00  1.00
ATOM     11  CB  ALA     1      -0.128   0.612  -1.663  1.00  1.00
ATOM     15  CRP ALA     1       0.823   0.801   0.637  1.00  1.00
ATOM     16  OR  ALA     1       1.969   0.367   0.665  1.00  1.00
ATOM     17  NR  ALA     1       0.477   1.912   1.333  1.00  1.00
ATOM     18  HR  ALA     1      -0.468   2.199   1.317  1.00  1.00
ATOM     19  CR  ALA     1       1.410   2.627   2.163  1.00  1.00
END
REMARK X=20 Y=21 
ATOM      1  CL  ALA     1      -3.113   1.661   1.504  1.00  1.00
ATOM      5  CLP ALA     1      -1.769   1.059   1.566  1.00  1.00
ATOM      6  OL  ALA     1      -1.201   0.940   2.629  1.00  1.00
ATOM      7  NL  ALA     1      -1.219   0.714   0.392  1.00  1.00
ATOM      8  HL  ALA     1      -1.742   0.797  -0.435  1.00  1.00
ATOM      9  CA  ALA     1       0.058   0.023   0.242  1.00  1.00
ATOM     10  HA  ALA     1      -0.001  -0.896   0.782  1.00  1.00
ATOM     11  CB  ALA     1       0.235  -0.295  -1.249  1.00  1.00
ATOM     15  CRP ALA     1       1.299   0.757   0.745  1.00  1.00
ATOM     16  OR  ALA     1       2.276   0.138   1.135  1.00  1.00
ATOM     17  NR  ALA     1       1.277   2.102   0.736  1.00  1.00
ATOM     18  HR  ALA     1       0.447   2.567   0.458  1.00  1.00
ATOM     19  CR  ALA     1       2.391   2.896   1.191  1.00  1.00
END
REMARK X=21 Y=22 
ATOM      1  CL  ALA     1      -3.089   1.850   1.546  1.00  1.00
ATOM      5  CLP ALA     1      -1.667   1.457   1.629  1.00  1.00
ATOM      6  OL  ALA     1      -0.974   1.868   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.204   0.683   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -1.844   0.360  -0.021  1.00  1.00
ATOM      9  CA  ALA     1       0.126   0.105   0.564  1.00  1.00
ATOM     10  HA  ALA     1       0.239  -0.555   1.391  1.00  1.00
ATOM     11  CB  ALA     1       0.215  -0.722  -0.739  1.00  1.00
ATOM     15  CRP ALA     1       1.311   1.068   0.623  1.00  1.00
ATOM     16  OR  ALA     1       2.369   0.726   1.149  1.00  1.00
ATOM     17  NR  ALA     1       1.156   2.292   0.077  1.00  1.00
ATOM     18  HR  ALA     1       0.273   2.549  -0.285  1.00  1.00
ATOM     19  CR  ALA     1       2.201   3.277   0.107  1.00  1.00
END
REMARK X=22 Y=23 
ATOM      1  CL  ALA     1      -3.102   1.775   1.619  1.00  1.00
ATOM      5  CLP ALA     1      -1.661   1.466   1.659  1.00  1.00
ATOM      6  OL  ALA     1      -0.945   1.961   2.476  1.00  1.00
ATOM      7  NL  ALA     1      -1.205   0.663   0.688  1.00  1.00
ATOM      8  HL  ALA     1      -1.854   0.269   0.091  1.00  1.00
ATOM      9  CA  ALA     1       0.147   0.134   0.561  1.00  1.00
ATOM     10  HA  ALA     1       0.300  -0.545   1.355  1.00  1.00
ATOM     11  CB  ALA     1       0.237  -0.632  -0.776  1.00  1.00
ATOM     15  CRP ALA     1       1.306   1.133   0.628  1.00  1.00
ATOM     16  OR  ALA     1       2.361   0.819   1.176  1.00  1.00
ATOM     17  NR  ALA     1       1.129   2.345   0.068  1.00  1.00
ATOM     18  HR  ALA     1       0.252   2.577  -0.315  1.00  1.00
ATOM     19  CR  ALA     1       2.150   3.364   0.108  1.00  1.00
END
REMARK X=23 Y=24 
ATOM      1  CL  ALA     1      -3.137   1.689   1.564  1.00  1.00
ATOM      5  CLP ALA     1      -1.674   1.466   1.595  1.00  1.00
ATOM      6  OL  ALA     1      -0.991   2.041   2.377  1.00  1.00
ATOM      7  NL  ALA     1      -1.178   0.640   0.664  1.00  1.00
ATOM      8  HL  ALA     1      -1.829   0.190   0.106  1.00  1.00
ATOM      9  CA  ALA     1       0.192   0.170   0.547  1.00  1.00
ATOM     10  HA  ALA     1       0.347  -0.550   1.313  1.00  1.00
ATOM     11  CB  ALA     1       0.333  -0.536  -0.821  1.00  1.00
ATOM     15  CRP ALA     1       1.325   1.194   0.686  1.00  1.00
ATOM     16  OR  ALA     1       2.348   0.906   1.293  1.00  1.00
ATOM     17  NR  ALA     1       1.165   2.398   0.103  1.00  1.00
ATOM     18  HR  ALA     1       0.311   2.617  -0.339  1.00  1.00
ATOM     19  CR  ALA     1       2.173   3.424   0.206  1.00  1.00
END
REMARK X=24 Y=25 
ATOM      1  CL  ALA     1      -3.342   1.726   1.297  1.00  1.00
ATOM      5  CLP ALA     1      -1.882   1.644   1.449  1.00  1.00
ATOM      6  OL  ALA     1      -1.296   2.423   2.124  1.00  1.00
ATOM      7  NL  ALA     1      -1.259   0.684   0.740  1.00  1.00
ATOM      8  HL  ALA     1      -1.839   0.091   0.256  1.00  1.00
ATOM      9  CA  ALA     1       0.138   0.295   0.784  1.00  1.00
ATOM     10  HA  ALA     1       0.267  -0.321   1.638  1.00  1.00
ATOM     11  CB  ALA     1       0.437  -0.541  -0.481  1.00  1.00
ATOM     15  CRP ALA     1       1.207   1.385   0.899  1.00  1.00
ATOM     16  OR  ALA     1       2.160   1.248   1.674  1.00  1.00
ATOM     17  NR  ALA     1       1.092   2.478   0.129  1.00  1.00
ATOM     18  HR  ALA     1       0.291   2.586  -0.440  1.00  1.00
ATOM     19  CR  ALA     1       2.044   3.567   0.190  1.00  1.00
END
REMARK X=25 Y=26 
ATOM      1  CL  ALA     1      -3.361   1.726   1.315  1.00  1.00
ATOM      5  CLP ALA     1      -1.890   1.687   1.423  1.00  1.00
ATOM      6  OL  ALA     1      -1.302   2.522   2.029  1.00  1.00
ATOM      7  NL  ALA     1      -1.285   0.691   0.757  1.00  1.00
ATOM      8  HL  ALA     1      -1.865   0.049   0.326  1.00  1.00
ATOM      9  CA  ALA     1       0.123   0.321   0.749  1.00  1.00
ATOM     10  HA  ALA     1       0.270  -0.331   1.585  1.00  1.00
ATOM     11  CB  ALA     1       0.408  -0.470  -0.534  1.00  1.00
ATOM     15  CRP ALA     1       1.192   1.410   0.900  1.00  1.00
ATOM     16  OR  ALA     1       2.114   1.273   1.701  1.00  1.00
ATOM     17  NR  ALA     1       1.111   2.493   0.112  1.00  1.00
ATOM     18  HR  ALA     1       0.326   2.609  -0.490  1.00  1.00
ATOM     19  CR  ALA     1       2.068   3.578   0.188  1.00  1.00
END
REMARK X=26 Y=27 
ATOM      1  CL  ALA     1      -3.419   1.747   1.251  1.00  1.00
ATOM      5  CLP ALA     1      -1.947   1.630   1.371  1.00  1.00
ATOM      6  OL  ALA     1      -1.331   2.379   2.060  1.00  1.00
ATOM      7  NL  ALA     1      -1.380   0.668   0.616  1.00  1.00
ATOM      8  HL  ALA     1      -1.992   0.115   0.104  1.00  1.00
ATOM      9  CA  ALA     1       0.007   0.227   0.571  1.00  1.00
ATOM     10  HA  ALA     1       0.086  -0.578   1.262  1.00  1.00
ATOM     11  CB  ALA     1       0.288  -0.306  -0.835  1.00  1.00
ATOM     15  CRP ALA     1       1.132   1.190   0.974  1.00  1.00
ATOM     16  OR  ALA     1       1.974   0.858   1.808  1.00  1.00
ATOM     17  NR  ALA     1       1.199   2.390   0.352  1.00  1.00
ATOM     18  HR  ALA     1       0.482   2.643  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.218   3.363   0.657  1.00  1.00
END
REMARK X=27 Y=28 
ATOM      1  CL  ALA     1      -3.430   1.748   1.261  1.00  1.00
ATOM      5  CLP ALA     1      -1.958   1.650   1.340  1.00  1.00
ATOM      6  OL  ALA     1      -1.333   2.471   1.961  1.00  1.00
ATOM      7  NL  ALA     1      -1.392   0.653   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -2.018   0.061   0.177  1.00  1.00
ATOM      9  CA  ALA     1      -0.005   0.219   0.569  1.00  1.00
ATOM     10  HA  ALA     1       0.083  -0.615   1.230  1.00  1.00
ATOM     11  CB  ALA     1       0.266  -0.275  -0.863  1.00  1.00
ATOM     15  CRP ALA     1       1.126   1.166   0.993  1.00  1.00
ATOM     16  OR  ALA     1       1.918   0.834   1.868  1.00  1.00
ATOM     17  NR  ALA     1       1.248   2.346   0.359  1.00  1.00
ATOM     18  HR  ALA     1       0.548   2.609  -0.299  1.00  1.00
ATOM     19  CR  ALA     1       2.271   3.308   0.675  1.00  1.00
END
REMARK X=28 Y=29 
ATOM      1  CL  ALA     1      -3.438   1.702   1.306  1.00  1.00
ATOM      5  CLP ALA     1      -1.962   1.659   1.317  1.00  1.00
ATOM      6  OL  ALA     1      -1.332   2.532   1.870  1.00  1.00
ATOM      7  NL  ALA     1      -1.406   0.632   0.671  1.00  1.00
ATOM      8  HL  ALA     1      -2.029   0.002   0.252  1.00  1.00
ATOM      9  CA  ALA     1      -0.007   0.228   0.554  1.00  1.00
ATOM     10  HA  ALA     1       0.103  -0.631   1.184  1.00  1.00
ATOM     11  CB  ALA     1       0.255  -0.224  -0.899  1.00  1.00
ATOM     15  CRP ALA     1       1.124   1.169   1.002  1.00  1.00
ATOM     16  OR  ALA     1       1.889   0.829   1.901  1.00  1.00
ATOM     17  NR  ALA     1       1.265   2.342   0.365  1.00  1.00
ATOM     18  HR  ALA     1       0.590   2.614  -0.306  1.00  1.00
ATOM     19  CR  ALA     1       2.313   3.280   0.698  1.00  1.00
END
REMARK X=29 Y=30 
ATOM      1  CL  ALA     1      -3.441   1.677   1.342  1.00  1.00
ATOM      5  CLP ALA     1      -1.971   1.666   1.304  1.00  1.00
ATOM      6  OL  ALA     1      -1.348   2.594   1.774  1.00  1.00
ATOM      7  NL  ALA     1      -1.408   0.602   0.696  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.062   0.329  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.235   0.538  1.00  1.00
ATOM     10  HA  ALA     1       0.114  -0.660   1.127  1.00  1.00
ATOM     11  CB  ALA     1       0.223  -0.161  -0.935  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.153   1.020  1.00  1.00
ATOM     16  OR  ALA     1       1.857   0.813   1.931  1.00  1.00
ATOM     17  NR  ALA     1       1.290   2.335   0.385  1.00  1.00
ATOM     18  HR  ALA     1       0.632   2.617  -0.298  1.00  1.00
ATOM     19  CR  ALA     1       2.337   3.252   0.749  1.00  1.00
END
REMARK X=30 Y=31 
ATOM      1  CL  ALA     1      -3.443   1.670   1.352  1.00  1.00
ATOM      5  CLP ALA     1      -1.973   1.670   1.295  1.00  1.00
ATOM      6  OL  ALA     1      -1.351   2.609   1.744  1.00  1.00
ATOM      7  NL  ALA     1      -1.409   0.597   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.076   0.355  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.237   0.533  1.00  1.00
ATOM     10  HA  ALA     1       0.119  -0.663   1.113  1.00  1.00
ATOM     11  CB  ALA     1       0.217  -0.147  -0.945  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.152   1.023  1.00  1.00
ATOM     16  OR  ALA     1       1.849   0.808   1.938  1.00  1.00
ATOM     17  NR  ALA     1       1.296   2.334   0.388  1.00  1.00
ATOM     18  HR  ALA     1       0.638   2.620  -0.293  1.00  1.00
ATOM     19  CR  ALA     1       2.342   3.249   0.754  1.00  1.00
END
REMARK X=31 Y=32 
ATOM      1  CL  ALA     1      -3.451   1.630   1.422  1.00  1.00
ATOM      5  CLP ALA     1      -1.983   1.689   1.248  1.00  1.00
ATOM      6  OL  ALA     1      -1.374   2.689   1.550  1.00  1.00
ATOM      7  NL  ALA     1      -1.421   0.569   0.756  1.00  1.00
ATOM      8  HL  ALA     1      -2.045  -0.151   0.513  1.00  1.00
ATOM      9  CA  ALA     1      -0.017   0.248   0.499  1.00  1.00
ATOM     10  HA  ALA     1       0.149  -0.681   1.023  1.00  1.00
ATOM     11  CB  ALA     1       0.171  -0.057  -0.999  1.00  1.00
ATOM     15  CRP ALA     1       1.111   1.147   1.033  1.00  1.00
ATOM     16  OR  ALA     1       1.807   0.781   1.969  1.00  1.00
ATOM     17  NR  ALA     1       1.327   2.329   0.410  1.00  1.00
ATOM     18  HR  ALA     1       0.679   2.635  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.372   3.237   0.799  1.00  1.00
END
REMARK X=32 Y=33 
ATOM      1  CL  ALA     1      -3.331   1.449   1.617  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.399   1.408  1.00  1.00
ATOM      6  OL  ALA     1      -1.169   2.255   1.904  1.00  1.00
ATOM      7  NL  ALA     1      -1.424   0.371   0.676  1.00  1.00
ATOM      8  HL  ALA     1      -2.118  -0.203   0.289  1.00  1.00
ATOM      9  CA  ALA     1      -0.062   0.001   0.310  1.00  1.00
ATOM     10  HA  ALA     1      -0.008  -1.054   0.497  1.00  1.00
ATOM     11  CB  ALA     1       0.131   0.162  -1.216  1.00  1.00
ATOM     15  CRP ALA     1       1.142   0.546   1.099  1.00  1.00
ATOM     16  OR  ALA     1       1.741  -0.171   1.894  1.00  1.00
ATOM     17  NR  ALA     1       1.537   1.815   0.864  1.00  1.00
ATOM     18  HR  ALA     1       0.963   2.391   0.297  1.00  1.00
ATOM     19  CR  ALA     1       2.669   2.426   1.513  1.00  1.00
END
REMARK X=33 Y=34 
ATOM      1  CL  ALA     1      -3.321   1.436   1.650  1.00  1.00
ATOM      5  CLP ALA     1      -1.870   1.422   1.372  1.00  1.00
ATOM      6  OL  ALA     1      -1.182   2.323   1.789  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.347   0.697  1.00  1.00
ATOM      8  HL  ALA     1      -2.106  -0.263   0.374  1.00  1.00
ATOM      9  CA  ALA     1      -0.057   0.008   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.002  -1.051   0.446  1.00  1.00
ATOM     11  CB  ALA     1       0.113   0.213  -1.212  1.00  1.00
ATOM     15  CRP ALA     1       1.139   0.538   1.102  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.196   1.881  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.803   0.879  1.00  1.00
ATOM     18  HR  ALA     1       0.972   2.397   0.326  1.00  1.00
ATOM     19  CR  ALA     1       2.672   2.407   1.539  1.00  1.00
END
REMARK X=34 Y=35 
ATOM      1  CL  ALA     1      -3.318   1.434   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -1.871   1.426   1.363  1.00  1.00
ATOM      6  OL  ALA     1      -1.186   2.341   1.756  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.343   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.101  -0.279   0.398  1.00  1.00
ATOM      9  CA  ALA     1      -0.058   0.010   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.005  -1.051   0.433  1.00  1.00
ATOM     11  CB  ALA     1       0.109   0.227  -1.215  1.00  1.00
ATOM     15  CRP ALA     1       1.138   0.536   1.100  1.00  1.00
ATOM     16  OR  ALA     1       1.723  -0.202   1.878  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.802   0.887  1.00  1.00
ATOM     18  HR  ALA     1       0.970   2.398   0.335  1.00  1.00
ATOM     19  CR  ALA     1       2.675   2.402   1.547  1.00  1.00
END
REMARK X=35 Y=36 
ATOM      1  CL  ALA     1      -3.297   1.417   1.700  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.437   1.310  1.00  1.00
ATOM      6  OL  ALA     1      -1.214   2.432   1.560  1.00  1.00
ATOM      7  NL  ALA     1      -1.412   0.320   0.746  1.00  1.00
ATOM      8  HL  ALA     1      -2.060  -0.372   0.544  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.025   0.282  1.00  1.00
ATOM     10  HA  ALA     1       0.023  -1.051   0.357  1.00  1.00
ATOM     11  CB  ALA     1       0.071   0.308  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.141   0.510   1.103  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.245   1.863  1.00  1.00
ATOM     17  NR  ALA     1       1.541   1.794   0.938  1.00  1.00
ATOM     18  HR  ALA     1       0.957   2.397   0.401  1.00  1.00
ATOM     19  CR  ALA     1       2.683   2.371   1.604  1.00  1.00
END
REMARK X=36 Y=37 
ATOM      1  CL  ALA     1      -3.283   1.421   1.730  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.449   1.277  1.00  1.00
ATOM      6  OL  ALA     1      -1.222   2.476   1.436  1.00  1.00
ATOM      7  NL  ALA     1      -1.405   0.299   0.773  1.00  1.00
ATOM      8  HL  ALA     1      -2.034  -0.422   0.640  1.00  1.00
ATOM      9  CA  ALA     1      -0.063   0.028   0.272  1.00  1.00
ATOM     10  HA  ALA     1       0.015  -1.050   0.307  1.00  1.00
ATOM     11  CB  ALA     1       0.057   0.364  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.134   0.492   1.093  1.00  1.00
ATOM     16  OR  ALA     1       1.729  -0.288   1.825  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.779   0.976  1.00  1.00
ATOM     18  HR  ALA     1       0.945   2.388   0.456  1.00  1.00
ATOM     19  CR  ALA     1       2.682   2.335   1.653  1.00  1.00
END
REMARK X=37 Y=38 
ATOM      1  CL  ALA     1      -3.265   1.435   1.760  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.457   1.257  1.00  1.00
ATOM      6  OL  ALA     1      -1.229   2.500   1.343  1.00  1.00
ATOM      7  NL  ALA     1      -1.398   0.292   0.802  1.00  1.00
ATOM      8  HL  ALA     1      -2.014  -0.454   0.728  1.00  1.00
ATOM      9  CA  ALA     1      -0.067   0.024   0.264  1.00  1.00
ATOM     10  HA  ALA     1       0.011  -1.049   0.257  1.00  1.00
ATOM     11  CB  ALA     1       0.028   0.426  -1.206  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.464   1.092  1.00  1.00
ATOM     16  OR  ALA     1       1.748  -0.346   1.781  1.00  1.00
ATOM     17  NR  ALA     1       1.532   1.754   1.029  1.00  1.00
ATOM     18  HR  ALA     1       0.931   2.385   0.536  1.00  1.00
ATOM     19  CR  ALA     1       2.676   2.280   1.721  1.00  1.00
END
REMARK X=38 Y=39 
ATOM      1  CL  ALA     1      -3.236   1.453   1.772  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.473   1.217  1.00  1.00
ATOM      6  OL  ALA     1      -1.244   2.522   1.222  1.00  1.00
ATOM      7  NL  ALA     1      -1.388   0.292   0.824  1.00  1.00
ATOM      8  HL  ALA     1      -1.982  -0.485   0.827  1.00  1.00
ATOM      9  CA  ALA     1      -0.066   0.031   0.248  1.00  1.00
ATOM     10  HA  ALA     1       0.018  -1.048   0.230  1.00  1.00
ATOM     11  CB  ALA     1       0.011   0.464  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.452   1.088  1.00  1.00
ATOM     16  OR  ALA     1       1.767  -0.373   1.737  1.00  1.00
ATOM     17  NR  ALA     1       1.517   1.749   1.061  1.00  1.00
ATOM     18  HR  ALA     1       0.906   2.387   0.586  1.00  1.00
ATOM     19  CR  ALA     1       2.660   2.262   1.754  1.00  1.00
END
REMARK X=39 Y=40 
ATOM      1  CL  ALA     1      -3.225   1.461   1.784  1.00  1.00
ATOM      5  CLP ALA     1      -1.878   1.466   1.191  1.00  1.00
ATOM      6  OL  ALA     1      -1.276   2.527   1.106  1.00  1.00
ATOM      7  NL  ALA     1      -1.375   0.274   0.839  1.00  1.00
ATOM      8  HL  ALA     1      -1.947  -0.517   0.921  1.00  1.00
ATOM      9  CA  ALA     1      -0.077   0.024   0.236  1.00  1.00
ATOM     10  HA  ALA     1       0.009  -1.048   0.194  1.00  1.00
ATOM     11  CB  ALA     1      -0.004   0.503  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.436   1.066  1.00  1.00
ATOM     16  OR  ALA     1       1.800  -0.403   1.678  1.00  1.00
ATOM     17  NR  ALA     1       1.483   1.736   1.091  1.00  1.00
ATOM     18  HR  ALA     1       0.861   2.388   0.647  1.00  1.00
ATOM     19  CR  ALA     1       2.642   2.246   1.792  1.00  1.00
END
REMARK X=40 Y=41 
ATOM      1  CL  ALA     1      -3.212   1.465   1.797  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.470   1.168  1.00  1.00
ATOM      6  OL  ALA     1      -1.286   2.526   1.008  1.00  1.00
ATOM      7  NL  ALA     1      -1.363   0.265   0.860  1.00  1.00
ATOM      8  HL  ALA     1      -1.914  -0.534   1.016  1.00  1.00
ATOM      9  CA  ALA     1      -0.074   0.012   0.232  1.00  1.00
ATOM     10  HA  ALA     1       0.001  -1.058   0.173  1.00  1.00
ATOM     11  CB  ALA     1      -0.020   0.528  -1.210  1.00  1.00
ATOM     15  CRP ALA     1       1.147   0.408   1.060  1.00  1.00
ATOM     16  OR  ALA     1       1.827  -0.445   1.625  1.00  1.00
ATOM     17  NR  ALA     1       1.461   1.721   1.140  1.00  1.00
ATOM     18  HR  ALA     1       0.821   2.361   0.731  1.00  1.00
ATOM     19  CR  ALA     1       2.614   2.214   1.845  1.00  1.00
END
REMARK X=41 Y=42 
ATOM      1  CL  ALA     1      -3.185   1.487   1.790  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.480   1.139  1.00  1.00
ATOM      6  OL  ALA     1      -1.293   2.532   0.896  1.00  1.00
ATOM      7  NL  ALA     1      -1.349   0.268   0.862  1.00  1.00
ATOM      8  HL  ALA     1      -1.881  -0.527   1.095  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.013   0.226  1.00  1.00
ATOM     10  HA  ALA     1      -0.006  -1.063   0.151  1.00  1.00
ATOM     11  CB  ALA     1      -0.019   0.539  -1.224  1.00  1.00
ATOM     15  CRP ALA     1       1.170   0.398   1.031  1.00  1.00
ATOM     16  OR  ALA     1       1.871  -0.463   1.540  1.00  1.00
ATOM     17  NR  ALA     1       1.447   1.706   1.159  1.00  1.00
ATOM     18  HR  ALA     1       0.788   2.362   0.800  1.00  1.00
ATOM     19  CR  ALA     1       2.602   2.205   1.868  1.00  1.00
END
REMARK X=42 Y=43 
ATOM      1  CL  ALA     1      -3.257   1.605   1.105  1.00  1.00
ATOM      5  CLP ALA     1      -1.941   1.459   0.447  1.00  1.00
ATOM      6  OL  ALA     1      -1.481   2.369  -0.223  1.00  1.00
ATOM      7  NL  ALA     1      -1.303   0.291   0.647  1.00  1.00
ATOM      8  HL  ALA     1      -1.743  -0.379   1.229  1.00  1.00
ATOM      9  CA  ALA     1      -0.011  -0.077   0.099  1.00  1.00
ATOM     10  HA  ALA     1       0.155  -1.099   0.417  1.00  1.00
ATOM     11  CB  ALA     1       0.001  -0.097  -1.439  1.00  1.00
ATOM     15  CRP ALA     1       1.191   0.673   0.683  1.00  1.00
ATOM     16  OR  ALA     1       2.015   0.103   1.375  1.00  1.00
ATOM     17  NR  ALA     1       1.303   1.983   0.393  1.00  1.00
ATOM     18  HR  ALA     1       0.553   2.411  -0.109  1.00  1.00
ATOM     19  CR  ALA     1       2.395   2.811   0.843  1.00  1.00
END
FIXED
  
Y: PDB2CONSTANTCreate a constant value from a PDB input file This action is a shortcut and uses the defaults shown here. More details ARGread this single argument from the input rather than the atomic structure=Y NOARGS the arguments that are being read from the PDB file are not in the plumed input REFERENCEa file in pdb format containing the reference structure=
regtest/trajectories/path_msd/allv.pdb
 Click here to see an extract from this file.
  
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FILE: regtest/trajectories/path_msd/allv.pdb
    
REMARK X=1 Y=2 
ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00
ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00
ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00
ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00
ATOM      8  HL  ALA     1      -1.845   0.961  -0.011  1.00  1.00
ATOM      9  CA  ALA     1      -0.003  -0.019   0.021  1.00  1.00
ATOM     10  HA  ALA     1       0.205  -1.051   0.259  1.00  1.00
ATOM     11  CB  ALA     1       0.009   0.135  -1.509  1.00  1.00
ATOM     15  CRP ALA     1       1.121   0.799   0.663  1.00  1.00
ATOM     16  OR  ALA     1       1.723   1.669   0.043  1.00  1.00
ATOM     17  NR  ALA     1       1.423   0.519   1.941  1.00  1.00
ATOM     18  HR  ALA     1       0.873  -0.161   2.413  1.00  1.00
ATOM     19  CR  ALA     1       2.477   1.187   2.675  1.00  1.00
END
FIXED
REMARK X=2 Y=3 
ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00
ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00
ATOM      6  OL  ALA     1      -1.201  -0.849   2.425  1.00  1.00
ATOM      7  NL  ALA     1      -1.296   0.337   0.534  1.00  1.00
ATOM      8  HL  ALA     1      -1.807   0.951  -0.044  1.00  1.00
ATOM      9  CA  ALA     1       0.009  -0.067   0.033  1.00  1.00
ATOM     10  HA  ALA     1       0.175  -1.105   0.283  1.00  1.00
ATOM     11  CB  ALA     1       0.027   0.046  -1.501  1.00  1.00
ATOM     15  CRP ALA     1       1.149   0.725   0.654  1.00  1.00
ATOM     16  OR  ALA     1       1.835   1.491  -0.011  1.00  1.00
ATOM     17  NR  ALA     1       1.380   0.537   1.968  1.00  1.00
ATOM     18  HR  ALA     1       0.764  -0.060   2.461  1.00  1.00
ATOM     19  CR  ALA     1       2.431   1.195   2.683  1.00  1.00
END
REMARK X=3 Y=4 
ATOM      1  CL  ALA     1      -2.990   0.383   2.277  1.00  1.00
ATOM      5  CLP ALA     1      -1.664  -0.085   1.831  1.00  1.00
ATOM      6  OL  ALA     1      -0.987  -0.835   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.227   0.364   0.646  1.00  1.00
ATOM      8  HL  ALA     1      -1.798   0.982   0.124  1.00  1.00
ATOM      9  CA  ALA     1       0.026  -0.028   0.044  1.00  1.00
ATOM     10  HA  ALA     1       0.224  -1.060   0.284  1.00  1.00
ATOM     11  CB  ALA     1      -0.076   0.107  -1.483  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.776   0.577  1.00  1.00
ATOM     16  OR  ALA     1       1.900   1.463  -0.158  1.00  1.00
ATOM     17  NR  ALA     1       1.494   0.666   1.888  1.00  1.00
ATOM     18  HR  ALA     1       0.882   0.122   2.437  1.00  1.00
ATOM     19  CR  ALA     1       2.580   1.341   2.529  1.00  1.00
END
REMARK X=4 Y=5 
ATOM      1  CL  ALA     1      -3.006   0.350   2.252  1.00  1.00
ATOM      5  CLP ALA     1      -1.680  -0.112   1.826  1.00  1.00
ATOM      6  OL  ALA     1      -1.025  -0.896   2.508  1.00  1.00
ATOM      7  NL  ALA     1      -1.220   0.368   0.654  1.00  1.00
ATOM      8  HL  ALA     1      -1.771   1.013   0.137  1.00  1.00
ATOM      9  CA  ALA     1       0.040  -0.029   0.062  1.00  1.00
ATOM     10  HA  ALA     1       0.210  -1.076   0.277  1.00  1.00
ATOM     11  CB  ALA     1      -0.066   0.148  -1.465  1.00  1.00
ATOM     15  CRP ALA     1       1.241   0.738   0.605  1.00  1.00
ATOM     16  OR  ALA     1       1.986   1.347  -0.125  1.00  1.00
ATOM     17  NR  ALA     1       1.446   0.694   1.940  1.00  1.00
ATOM     18  HR  ALA     1       0.796   0.210   2.481  1.00  1.00
ATOM     19  CR  ALA     1       2.544   1.350   2.582  1.00  1.00
END
REMARK X=5 Y=6 
ATOM      1  CL  ALA     1      -3.002   0.343   2.271  1.00  1.00
ATOM      5  CLP ALA     1      -1.672  -0.125   1.828  1.00  1.00
ATOM      6  OL  ALA     1      -1.028  -0.942   2.486  1.00  1.00
ATOM      7  NL  ALA     1      -1.213   0.373   0.670  1.00  1.00
ATOM      8  HL  ALA     1      -1.752   1.033   0.169  1.00  1.00
ATOM      9  CA  ALA     1       0.041  -0.032   0.055  1.00  1.00
ATOM     10  HA  ALA     1       0.201  -1.079   0.245  1.00  1.00
ATOM     11  CB  ALA     1      -0.079   0.194  -1.466  1.00  1.00
ATOM     15  CRP ALA     1       1.257   0.720   0.601  1.00  1.00
ATOM     16  OR  ALA     1       2.057   1.240  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.422   0.730   1.942  1.00  1.00
ATOM     18  HR  ALA     1       0.740   0.303   2.500  1.00  1.00
ATOM     19  CR  ALA     1       2.528   1.373   2.598  1.00  1.00
END
REMARK X=6 Y=7 
ATOM      1  CL  ALA     1      -3.144   1.457   1.417  1.00  1.00
ATOM      5  CLP ALA     1      -1.943   0.587   1.450  1.00  1.00
ATOM      6  OL  ALA     1      -1.588   0.028   2.480  1.00  1.00
ATOM      7  NL  ALA     1      -1.281   0.449   0.306  1.00  1.00
ATOM      8  HL  ALA     1      -1.578   0.914  -0.520  1.00  1.00
ATOM      9  CA  ALA     1      -0.132  -0.428   0.139  1.00  1.00
ATOM     10  HA  ALA     1      -0.264  -1.291   0.758  1.00  1.00
ATOM     11  CB  ALA     1      -0.066  -0.855  -1.329  1.00  1.00
ATOM     15  CRP ALA     1       1.193   0.220   0.554  1.00  1.00
ATOM     16  OR  ALA     1       2.195   0.098  -0.140  1.00  1.00
ATOM     17  NR  ALA     1       1.224   0.872   1.737  1.00  1.00
ATOM     18  HR  ALA     1       0.399   0.943   2.273  1.00  1.00
ATOM     19  CR  ALA     1       2.413   1.511   2.254  1.00  1.00
END
REMARK X=7 Y=8 
ATOM      1  CL  ALA     1      -3.140   1.441   1.453  1.00  1.00
ATOM      5  CLP ALA     1      -1.944   0.576   1.465  1.00  1.00
ATOM      6  OL  ALA     1      -1.587  -0.018   2.487  1.00  1.00
ATOM      7  NL  ALA     1      -1.274   0.465   0.322  1.00  1.00
ATOM      8  HL  ALA     1      -1.571   0.957  -0.486  1.00  1.00
ATOM      9  CA  ALA     1      -0.124  -0.418   0.135  1.00  1.00
ATOM     10  HA  ALA     1      -0.274  -1.304   0.729  1.00  1.00
ATOM     11  CB  ALA     1      -0.063  -0.813  -1.347  1.00  1.00
ATOM     15  CRP ALA     1       1.201   0.199   0.572  1.00  1.00
ATOM     16  OR  ALA     1       2.227   0.007  -0.072  1.00  1.00
ATOM     17  NR  ALA     1       1.215   0.910   1.709  1.00  1.00
ATOM     18  HR  ALA     1       0.369   1.020   2.200  1.00  1.00
ATOM     19  CR  ALA     1       2.393   1.536   2.237  1.00  1.00
END
REMARK X=8 Y=9 
ATOM      1  CL  ALA     1      -3.140   1.420   1.442  1.00  1.00
ATOM      5  CLP ALA     1      -1.948   0.546   1.448  1.00  1.00
ATOM      6  OL  ALA     1      -1.618  -0.065   2.460  1.00  1.00
ATOM      7  NL  ALA     1      -1.255   0.469   0.311  1.00  1.00
ATOM      8  HL  ALA     1      -1.538   0.979  -0.490  1.00  1.00
ATOM      9  CA  ALA     1      -0.107  -0.412   0.124  1.00  1.00
ATOM     10  HA  ALA     1      -0.257  -1.312   0.685  1.00  1.00
ATOM     11  CB  ALA     1      -0.028  -0.770  -1.375  1.00  1.00
ATOM     15  CRP ALA     1       1.217   0.186   0.600  1.00  1.00
ATOM     16  OR  ALA     1       2.269  -0.069   0.026  1.00  1.00
ATOM     17  NR  ALA     1       1.193   0.966   1.687  1.00  1.00
ATOM     18  HR  ALA     1       0.333   1.114   2.120  1.00  1.00
ATOM     19  CR  ALA     1       2.377   1.589   2.240  1.00  1.00
END
REMARK X=9 Y=10 
ATOM      1  CL  ALA     1      -3.110   1.698   0.880  1.00  1.00
ATOM      5  CLP ALA     1      -2.021   0.734   1.142  1.00  1.00
ATOM      6  OL  ALA     1      -1.859   0.257   2.258  1.00  1.00
ATOM      7  NL  ALA     1      -1.229   0.414   0.114  1.00  1.00
ATOM      8  HL  ALA     1      -1.371   0.826  -0.771  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.593   0.188  1.00  1.00
ATOM     10  HA  ALA     1      -0.481  -1.374   0.851  1.00  1.00
ATOM     11  CB  ALA     1       0.011  -1.180  -1.220  1.00  1.00
ATOM     15  CRP ALA     1       1.163  -0.060   0.716  1.00  1.00
ATOM     16  OR  ALA     1       2.227  -0.564   0.393  1.00  1.00
ATOM     17  NR  ALA     1       1.127   0.960   1.594  1.00  1.00
ATOM     18  HR  ALA     1       0.234   1.295   1.847  1.00  1.00
ATOM     19  CR  ALA     1       2.303   1.549   2.172  1.00  1.00
END
REMARK X=10 Y=11 
ATOM      1  CL  ALA     1      -3.139   1.652   0.924  1.00  1.00
ATOM      5  CLP ALA     1      -2.039   0.698   1.169  1.00  1.00
ATOM      6  OL  ALA     1      -1.868   0.201   2.278  1.00  1.00
ATOM      7  NL  ALA     1      -1.239   0.411   0.139  1.00  1.00
ATOM      8  HL  ALA     1      -1.385   0.842  -0.737  1.00  1.00
ATOM      9  CA  ALA     1      -0.173  -0.574   0.193  1.00  1.00
ATOM     10  HA  ALA     1      -0.477  -1.381   0.833  1.00  1.00
ATOM     11  CB  ALA     1       0.029  -1.142  -1.231  1.00  1.00
ATOM     15  CRP ALA     1       1.162  -0.048   0.731  1.00  1.00
ATOM     16  OR  ALA     1       2.220  -0.597   0.472  1.00  1.00
ATOM     17  NR  ALA     1       1.122   1.024   1.537  1.00  1.00
ATOM     18  HR  ALA     1       0.233   1.395   1.752  1.00  1.00
ATOM     19  CR  ALA     1       2.300   1.629   2.102  1.00  1.00
END
REMARK X=11 Y=12 
ATOM      1  CL  ALA     1      -3.706   1.088   0.468  1.00  1.00
ATOM      5  CLP ALA     1      -2.458   0.598   1.082  1.00  1.00
ATOM      6  OL  ALA     1      -2.390   0.404   2.277  1.00  1.00
ATOM      7  NL  ALA     1      -1.427   0.382   0.258  1.00  1.00
ATOM      8  HL  ALA     1      -1.513   0.559  -0.713  1.00  1.00
ATOM      9  CA  ALA     1      -0.157  -0.192   0.685  1.00  1.00
ATOM     10  HA  ALA     1      -0.343  -0.912   1.470  1.00  1.00
ATOM     11  CB  ALA     1       0.462  -0.936  -0.512  1.00  1.00
ATOM     15  CRP ALA     1       0.840   0.814   1.241  1.00  1.00
ATOM     16  OR  ALA     1       2.034   0.549   1.354  1.00  1.00
ATOM     17  NR  ALA     1       0.368   2.017   1.650  1.00  1.00
ATOM     18  HR  ALA     1      -0.613   2.169   1.589  1.00  1.00
ATOM     19  CR  ALA     1       1.215   3.044   2.195  1.00  1.00
END
REMARK X=12 Y=13 
ATOM      1  CL  ALA     1      -3.699   1.173   0.487  1.00  1.00
ATOM      5  CLP ALA     1      -2.464   0.631   1.079  1.00  1.00
ATOM      6  OL  ALA     1      -2.402   0.386   2.275  1.00  1.00
ATOM      7  NL  ALA     1      -1.434   0.437   0.260  1.00  1.00
ATOM      8  HL  ALA     1      -1.516   0.652  -0.701  1.00  1.00
ATOM      9  CA  ALA     1      -0.174  -0.174   0.667  1.00  1.00
ATOM     10  HA  ALA     1      -0.377  -0.924   1.411  1.00  1.00
ATOM     11  CB  ALA     1       0.451  -0.859  -0.570  1.00  1.00
ATOM     15  CRP ALA     1       0.839   0.801   1.280  1.00  1.00
ATOM     16  OR  ALA     1       1.999   0.474   1.468  1.00  1.00
ATOM     17  NR  ALA     1       0.404   2.024   1.627  1.00  1.00
ATOM     18  HR  ALA     1      -0.565   2.225   1.505  1.00  1.00
ATOM     19  CR  ALA     1       1.262   3.025   2.214  1.00  1.00
END
REMARK X=13 Y=14 
ATOM      1  CL  ALA     1      -3.653   0.990   1.121  1.00  1.00
ATOM      5  CLP ALA     1      -2.321   0.364   1.249  1.00  1.00
ATOM      6  OL  ALA     1      -2.006  -0.222   2.265  1.00  1.00
ATOM      7  NL  ALA     1      -1.498   0.501   0.205  1.00  1.00
ATOM      8  HL  ALA     1      -1.794   0.978  -0.603  1.00  1.00
ATOM      9  CA  ALA     1      -0.190  -0.127   0.128  1.00  1.00
ATOM     10  HA  ALA     1      -0.216  -1.086   0.627  1.00  1.00
ATOM     11  CB  ALA     1       0.159  -0.359  -1.359  1.00  1.00
ATOM     15  CRP ALA     1       0.933   0.668   0.793  1.00  1.00
ATOM     16  OR  ALA     1       2.107   0.313   0.705  1.00  1.00
ATOM     17  NR  ALA     1       0.604   1.770   1.498  1.00  1.00
ATOM     18  HR  ALA     1      -0.359   1.986   1.593  1.00  1.00
ATOM     19  CR  ALA     1       1.573   2.595   2.158  1.00  1.00
END
REMARK X=14 Y=15 
ATOM      1  CL  ALA     1      -3.641   0.954   1.179  1.00  1.00
ATOM      5  CLP ALA     1      -2.294   0.335   1.290  1.00  1.00
ATOM      6  OL  ALA     1      -1.964  -0.273   2.288  1.00  1.00
ATOM      7  NL  ALA     1      -1.485   0.499   0.235  1.00  1.00
ATOM      8  HL  ALA     1      -1.803   0.995  -0.564  1.00  1.00
ATOM      9  CA  ALA     1      -0.175  -0.118   0.130  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.077   0.601  1.00  1.00
ATOM     11  CB  ALA     1       0.162  -0.300  -1.355  1.00  1.00
ATOM     15  CRP ALA     1       0.952   0.671   0.815  1.00  1.00
ATOM     16  OR  ALA     1       2.104   0.260   0.791  1.00  1.00
ATOM     17  NR  ALA     1       0.633   1.808   1.450  1.00  1.00
ATOM     18  HR  ALA     1      -0.328   2.065   1.503  1.00  1.00
ATOM     19  CR  ALA     1       1.608   2.627   2.129  1.00  1.00
END
REMARK X=15 Y=16 
ATOM      1  CL  ALA     1      -3.635   0.925   1.244  1.00  1.00
ATOM      5  CLP ALA     1      -2.297   0.305   1.309  1.00  1.00
ATOM      6  OL  ALA     1      -1.941  -0.334   2.290  1.00  1.00
ATOM      7  NL  ALA     1      -1.500   0.490   0.251  1.00  1.00
ATOM      8  HL  ALA     1      -1.827   1.009  -0.537  1.00  1.00
ATOM      9  CA  ALA     1      -0.178  -0.110   0.119  1.00  1.00
ATOM     10  HA  ALA     1      -0.205  -1.094   0.536  1.00  1.00
ATOM     11  CB  ALA     1       0.147  -0.217  -1.379  1.00  1.00
ATOM     15  CRP ALA     1       0.943   0.643   0.832  1.00  1.00
ATOM     16  OR  ALA     1       2.074   0.198   0.871  1.00  1.00
ATOM     17  NR  ALA     1       0.637   1.821   1.423  1.00  1.00
ATOM     18  HR  ALA     1      -0.311   2.123   1.418  1.00  1.00
ATOM     19  CR  ALA     1       1.602   2.629   2.109  1.00  1.00
END
REMARK X=16 Y=17 
ATOM      1  CL  ALA     1      -3.632   0.856   1.331  1.00  1.00
ATOM      5  CLP ALA     1      -2.282   0.250   1.355  1.00  1.00
ATOM      6  OL  ALA     1      -1.906  -0.403   2.301  1.00  1.00
ATOM      7  NL  ALA     1      -1.515   0.478   0.275  1.00  1.00
ATOM      8  HL  ALA     1      -1.860   0.990  -0.485  1.00  1.00
ATOM      9  CA  ALA     1      -0.192  -0.105   0.098  1.00  1.00
ATOM     10  HA  ALA     1      -0.204  -1.121   0.473  1.00  1.00
ATOM     11  CB  ALA     1       0.129  -0.136  -1.408  1.00  1.00
ATOM     15  CRP ALA     1       0.931   0.615   0.844  1.00  1.00
ATOM     16  OR  ALA     1       2.043   0.122   0.934  1.00  1.00
ATOM     17  NR  ALA     1       0.651   1.819   1.388  1.00  1.00
ATOM     18  HR  ALA     1      -0.283   2.155   1.349  1.00  1.00
ATOM     19  CR  ALA     1       1.624   2.595   2.115  1.00  1.00
END
REMARK X=17 Y=18 
ATOM      1  CL  ALA     1      -3.628   0.823   1.358  1.00  1.00
ATOM      5  CLP ALA     1      -2.277   0.241   1.370  1.00  1.00
ATOM      6  OL  ALA     1      -1.871  -0.396   2.325  1.00  1.00
ATOM      7  NL  ALA     1      -1.525   0.469   0.284  1.00  1.00
ATOM      8  HL  ALA     1      -1.898   0.970  -0.482  1.00  1.00
ATOM      9  CA  ALA     1      -0.195  -0.094   0.086  1.00  1.00
ATOM     10  HA  ALA     1      -0.203  -1.122   0.423  1.00  1.00
ATOM     11  CB  ALA     1       0.146  -0.058  -1.413  1.00  1.00
ATOM     15  CRP ALA     1       0.919   0.599   0.874  1.00  1.00
ATOM     16  OR  ALA     1       1.997   0.065   1.039  1.00  1.00
ATOM     17  NR  ALA     1       0.655   1.830   1.373  1.00  1.00
ATOM     18  HR  ALA     1      -0.248   2.200   1.261  1.00  1.00
ATOM     19  CR  ALA     1       1.625   2.581   2.124  1.00  1.00
END
REMARK X=18 Y=19 
ATOM      1  CL  ALA     1      -3.539   0.055   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -2.117  -0.208   1.378  1.00  1.00
ATOM      6  OL  ALA     1      -1.453  -0.902   2.125  1.00  1.00
ATOM      7  NL  ALA     1      -1.602   0.351   0.289  1.00  1.00
ATOM      8  HL  ALA     1      -2.185   0.875  -0.310  1.00  1.00
ATOM      9  CA  ALA     1      -0.243   0.129  -0.186  1.00  1.00
ATOM     10  HA  ALA     1      -0.041  -0.924  -0.159  1.00  1.00
ATOM     11  CB  ALA     1      -0.153   0.625  -1.651  1.00  1.00
ATOM     15  CRP ALA     1       0.852   0.806   0.637  1.00  1.00
ATOM     16  OR  ALA     1       2.007   0.400   0.594  1.00  1.00
ATOM     17  NR  ALA     1       0.508   1.855   1.401  1.00  1.00
ATOM     18  HR  ALA     1      -0.445   2.112   1.454  1.00  1.00
ATOM     19  CR  ALA     1       1.460   2.569   2.226  1.00  1.00
END
REMARK X=19 Y=20 
ATOM      1  CL  ALA     1      -3.578   0.084   1.603  1.00  1.00
ATOM      5  CLP ALA     1      -2.140  -0.156   1.375  1.00  1.00
ATOM      6  OL  ALA     1      -1.473  -0.732   2.197  1.00  1.00
ATOM      7  NL  ALA     1      -1.623   0.335   0.237  1.00  1.00
ATOM      8  HL  ALA     1      -2.220   0.753  -0.416  1.00  1.00
ATOM      9  CA  ALA     1      -0.253   0.120  -0.195  1.00  1.00
ATOM     10  HA  ALA     1      -0.048  -0.931  -0.153  1.00  1.00
ATOM     11  CB  ALA     1      -0.128   0.612  -1.663  1.00  1.00
ATOM     15  CRP ALA     1       0.823   0.801   0.637  1.00  1.00
ATOM     16  OR  ALA     1       1.969   0.367   0.665  1.00  1.00
ATOM     17  NR  ALA     1       0.477   1.912   1.333  1.00  1.00
ATOM     18  HR  ALA     1      -0.468   2.199   1.317  1.00  1.00
ATOM     19  CR  ALA     1       1.410   2.627   2.163  1.00  1.00
END
REMARK X=20 Y=21 
ATOM      1  CL  ALA     1      -3.113   1.661   1.504  1.00  1.00
ATOM      5  CLP ALA     1      -1.769   1.059   1.566  1.00  1.00
ATOM      6  OL  ALA     1      -1.201   0.940   2.629  1.00  1.00
ATOM      7  NL  ALA     1      -1.219   0.714   0.392  1.00  1.00
ATOM      8  HL  ALA     1      -1.742   0.797  -0.435  1.00  1.00
ATOM      9  CA  ALA     1       0.058   0.023   0.242  1.00  1.00
ATOM     10  HA  ALA     1      -0.001  -0.896   0.782  1.00  1.00
ATOM     11  CB  ALA     1       0.235  -0.295  -1.249  1.00  1.00
ATOM     15  CRP ALA     1       1.299   0.757   0.745  1.00  1.00
ATOM     16  OR  ALA     1       2.276   0.138   1.135  1.00  1.00
ATOM     17  NR  ALA     1       1.277   2.102   0.736  1.00  1.00
ATOM     18  HR  ALA     1       0.447   2.567   0.458  1.00  1.00
ATOM     19  CR  ALA     1       2.391   2.896   1.191  1.00  1.00
END
REMARK X=21 Y=22 
ATOM      1  CL  ALA     1      -3.089   1.850   1.546  1.00  1.00
ATOM      5  CLP ALA     1      -1.667   1.457   1.629  1.00  1.00
ATOM      6  OL  ALA     1      -0.974   1.868   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.204   0.683   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -1.844   0.360  -0.021  1.00  1.00
ATOM      9  CA  ALA     1       0.126   0.105   0.564  1.00  1.00
ATOM     10  HA  ALA     1       0.239  -0.555   1.391  1.00  1.00
ATOM     11  CB  ALA     1       0.215  -0.722  -0.739  1.00  1.00
ATOM     15  CRP ALA     1       1.311   1.068   0.623  1.00  1.00
ATOM     16  OR  ALA     1       2.369   0.726   1.149  1.00  1.00
ATOM     17  NR  ALA     1       1.156   2.292   0.077  1.00  1.00
ATOM     18  HR  ALA     1       0.273   2.549  -0.285  1.00  1.00
ATOM     19  CR  ALA     1       2.201   3.277   0.107  1.00  1.00
END
REMARK X=22 Y=23 
ATOM      1  CL  ALA     1      -3.102   1.775   1.619  1.00  1.00
ATOM      5  CLP ALA     1      -1.661   1.466   1.659  1.00  1.00
ATOM      6  OL  ALA     1      -0.945   1.961   2.476  1.00  1.00
ATOM      7  NL  ALA     1      -1.205   0.663   0.688  1.00  1.00
ATOM      8  HL  ALA     1      -1.854   0.269   0.091  1.00  1.00
ATOM      9  CA  ALA     1       0.147   0.134   0.561  1.00  1.00
ATOM     10  HA  ALA     1       0.300  -0.545   1.355  1.00  1.00
ATOM     11  CB  ALA     1       0.237  -0.632  -0.776  1.00  1.00
ATOM     15  CRP ALA     1       1.306   1.133   0.628  1.00  1.00
ATOM     16  OR  ALA     1       2.361   0.819   1.176  1.00  1.00
ATOM     17  NR  ALA     1       1.129   2.345   0.068  1.00  1.00
ATOM     18  HR  ALA     1       0.252   2.577  -0.315  1.00  1.00
ATOM     19  CR  ALA     1       2.150   3.364   0.108  1.00  1.00
END
REMARK X=23 Y=24 
ATOM      1  CL  ALA     1      -3.137   1.689   1.564  1.00  1.00
ATOM      5  CLP ALA     1      -1.674   1.466   1.595  1.00  1.00
ATOM      6  OL  ALA     1      -0.991   2.041   2.377  1.00  1.00
ATOM      7  NL  ALA     1      -1.178   0.640   0.664  1.00  1.00
ATOM      8  HL  ALA     1      -1.829   0.190   0.106  1.00  1.00
ATOM      9  CA  ALA     1       0.192   0.170   0.547  1.00  1.00
ATOM     10  HA  ALA     1       0.347  -0.550   1.313  1.00  1.00
ATOM     11  CB  ALA     1       0.333  -0.536  -0.821  1.00  1.00
ATOM     15  CRP ALA     1       1.325   1.194   0.686  1.00  1.00
ATOM     16  OR  ALA     1       2.348   0.906   1.293  1.00  1.00
ATOM     17  NR  ALA     1       1.165   2.398   0.103  1.00  1.00
ATOM     18  HR  ALA     1       0.311   2.617  -0.339  1.00  1.00
ATOM     19  CR  ALA     1       2.173   3.424   0.206  1.00  1.00
END
REMARK X=24 Y=25 
ATOM      1  CL  ALA     1      -3.342   1.726   1.297  1.00  1.00
ATOM      5  CLP ALA     1      -1.882   1.644   1.449  1.00  1.00
ATOM      6  OL  ALA     1      -1.296   2.423   2.124  1.00  1.00
ATOM      7  NL  ALA     1      -1.259   0.684   0.740  1.00  1.00
ATOM      8  HL  ALA     1      -1.839   0.091   0.256  1.00  1.00
ATOM      9  CA  ALA     1       0.138   0.295   0.784  1.00  1.00
ATOM     10  HA  ALA     1       0.267  -0.321   1.638  1.00  1.00
ATOM     11  CB  ALA     1       0.437  -0.541  -0.481  1.00  1.00
ATOM     15  CRP ALA     1       1.207   1.385   0.899  1.00  1.00
ATOM     16  OR  ALA     1       2.160   1.248   1.674  1.00  1.00
ATOM     17  NR  ALA     1       1.092   2.478   0.129  1.00  1.00
ATOM     18  HR  ALA     1       0.291   2.586  -0.440  1.00  1.00
ATOM     19  CR  ALA     1       2.044   3.567   0.190  1.00  1.00
END
REMARK X=25 Y=26 
ATOM      1  CL  ALA     1      -3.361   1.726   1.315  1.00  1.00
ATOM      5  CLP ALA     1      -1.890   1.687   1.423  1.00  1.00
ATOM      6  OL  ALA     1      -1.302   2.522   2.029  1.00  1.00
ATOM      7  NL  ALA     1      -1.285   0.691   0.757  1.00  1.00
ATOM      8  HL  ALA     1      -1.865   0.049   0.326  1.00  1.00
ATOM      9  CA  ALA     1       0.123   0.321   0.749  1.00  1.00
ATOM     10  HA  ALA     1       0.270  -0.331   1.585  1.00  1.00
ATOM     11  CB  ALA     1       0.408  -0.470  -0.534  1.00  1.00
ATOM     15  CRP ALA     1       1.192   1.410   0.900  1.00  1.00
ATOM     16  OR  ALA     1       2.114   1.273   1.701  1.00  1.00
ATOM     17  NR  ALA     1       1.111   2.493   0.112  1.00  1.00
ATOM     18  HR  ALA     1       0.326   2.609  -0.490  1.00  1.00
ATOM     19  CR  ALA     1       2.068   3.578   0.188  1.00  1.00
END
REMARK X=26 Y=27 
ATOM      1  CL  ALA     1      -3.419   1.747   1.251  1.00  1.00
ATOM      5  CLP ALA     1      -1.947   1.630   1.371  1.00  1.00
ATOM      6  OL  ALA     1      -1.331   2.379   2.060  1.00  1.00
ATOM      7  NL  ALA     1      -1.380   0.668   0.616  1.00  1.00
ATOM      8  HL  ALA     1      -1.992   0.115   0.104  1.00  1.00
ATOM      9  CA  ALA     1       0.007   0.227   0.571  1.00  1.00
ATOM     10  HA  ALA     1       0.086  -0.578   1.262  1.00  1.00
ATOM     11  CB  ALA     1       0.288  -0.306  -0.835  1.00  1.00
ATOM     15  CRP ALA     1       1.132   1.190   0.974  1.00  1.00
ATOM     16  OR  ALA     1       1.974   0.858   1.808  1.00  1.00
ATOM     17  NR  ALA     1       1.199   2.390   0.352  1.00  1.00
ATOM     18  HR  ALA     1       0.482   2.643  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.218   3.363   0.657  1.00  1.00
END
REMARK X=27 Y=28 
ATOM      1  CL  ALA     1      -3.430   1.748   1.261  1.00  1.00
ATOM      5  CLP ALA     1      -1.958   1.650   1.340  1.00  1.00
ATOM      6  OL  ALA     1      -1.333   2.471   1.961  1.00  1.00
ATOM      7  NL  ALA     1      -1.392   0.653   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -2.018   0.061   0.177  1.00  1.00
ATOM      9  CA  ALA     1      -0.005   0.219   0.569  1.00  1.00
ATOM     10  HA  ALA     1       0.083  -0.615   1.230  1.00  1.00
ATOM     11  CB  ALA     1       0.266  -0.275  -0.863  1.00  1.00
ATOM     15  CRP ALA     1       1.126   1.166   0.993  1.00  1.00
ATOM     16  OR  ALA     1       1.918   0.834   1.868  1.00  1.00
ATOM     17  NR  ALA     1       1.248   2.346   0.359  1.00  1.00
ATOM     18  HR  ALA     1       0.548   2.609  -0.299  1.00  1.00
ATOM     19  CR  ALA     1       2.271   3.308   0.675  1.00  1.00
END
REMARK X=28 Y=29 
ATOM      1  CL  ALA     1      -3.438   1.702   1.306  1.00  1.00
ATOM      5  CLP ALA     1      -1.962   1.659   1.317  1.00  1.00
ATOM      6  OL  ALA     1      -1.332   2.532   1.870  1.00  1.00
ATOM      7  NL  ALA     1      -1.406   0.632   0.671  1.00  1.00
ATOM      8  HL  ALA     1      -2.029   0.002   0.252  1.00  1.00
ATOM      9  CA  ALA     1      -0.007   0.228   0.554  1.00  1.00
ATOM     10  HA  ALA     1       0.103  -0.631   1.184  1.00  1.00
ATOM     11  CB  ALA     1       0.255  -0.224  -0.899  1.00  1.00
ATOM     15  CRP ALA     1       1.124   1.169   1.002  1.00  1.00
ATOM     16  OR  ALA     1       1.889   0.829   1.901  1.00  1.00
ATOM     17  NR  ALA     1       1.265   2.342   0.365  1.00  1.00
ATOM     18  HR  ALA     1       0.590   2.614  -0.306  1.00  1.00
ATOM     19  CR  ALA     1       2.313   3.280   0.698  1.00  1.00
END
REMARK X=29 Y=30 
ATOM      1  CL  ALA     1      -3.441   1.677   1.342  1.00  1.00
ATOM      5  CLP ALA     1      -1.971   1.666   1.304  1.00  1.00
ATOM      6  OL  ALA     1      -1.348   2.594   1.774  1.00  1.00
ATOM      7  NL  ALA     1      -1.408   0.602   0.696  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.062   0.329  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.235   0.538  1.00  1.00
ATOM     10  HA  ALA     1       0.114  -0.660   1.127  1.00  1.00
ATOM     11  CB  ALA     1       0.223  -0.161  -0.935  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.153   1.020  1.00  1.00
ATOM     16  OR  ALA     1       1.857   0.813   1.931  1.00  1.00
ATOM     17  NR  ALA     1       1.290   2.335   0.385  1.00  1.00
ATOM     18  HR  ALA     1       0.632   2.617  -0.298  1.00  1.00
ATOM     19  CR  ALA     1       2.337   3.252   0.749  1.00  1.00
END
REMARK X=30 Y=31 
ATOM      1  CL  ALA     1      -3.443   1.670   1.352  1.00  1.00
ATOM      5  CLP ALA     1      -1.973   1.670   1.295  1.00  1.00
ATOM      6  OL  ALA     1      -1.351   2.609   1.744  1.00  1.00
ATOM      7  NL  ALA     1      -1.409   0.597   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.050  -0.076   0.355  1.00  1.00
ATOM      9  CA  ALA     1      -0.014   0.237   0.533  1.00  1.00
ATOM     10  HA  ALA     1       0.119  -0.663   1.113  1.00  1.00
ATOM     11  CB  ALA     1       0.217  -0.147  -0.945  1.00  1.00
ATOM     15  CRP ALA     1       1.115   1.152   1.023  1.00  1.00
ATOM     16  OR  ALA     1       1.849   0.808   1.938  1.00  1.00
ATOM     17  NR  ALA     1       1.296   2.334   0.388  1.00  1.00
ATOM     18  HR  ALA     1       0.638   2.620  -0.293  1.00  1.00
ATOM     19  CR  ALA     1       2.342   3.249   0.754  1.00  1.00
END
REMARK X=31 Y=32 
ATOM      1  CL  ALA     1      -3.451   1.630   1.422  1.00  1.00
ATOM      5  CLP ALA     1      -1.983   1.689   1.248  1.00  1.00
ATOM      6  OL  ALA     1      -1.374   2.689   1.550  1.00  1.00
ATOM      7  NL  ALA     1      -1.421   0.569   0.756  1.00  1.00
ATOM      8  HL  ALA     1      -2.045  -0.151   0.513  1.00  1.00
ATOM      9  CA  ALA     1      -0.017   0.248   0.499  1.00  1.00
ATOM     10  HA  ALA     1       0.149  -0.681   1.023  1.00  1.00
ATOM     11  CB  ALA     1       0.171  -0.057  -0.999  1.00  1.00
ATOM     15  CRP ALA     1       1.111   1.147   1.033  1.00  1.00
ATOM     16  OR  ALA     1       1.807   0.781   1.969  1.00  1.00
ATOM     17  NR  ALA     1       1.327   2.329   0.410  1.00  1.00
ATOM     18  HR  ALA     1       0.679   2.635  -0.277  1.00  1.00
ATOM     19  CR  ALA     1       2.372   3.237   0.799  1.00  1.00
END
REMARK X=32 Y=33 
ATOM      1  CL  ALA     1      -3.331   1.449   1.617  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.399   1.408  1.00  1.00
ATOM      6  OL  ALA     1      -1.169   2.255   1.904  1.00  1.00
ATOM      7  NL  ALA     1      -1.424   0.371   0.676  1.00  1.00
ATOM      8  HL  ALA     1      -2.118  -0.203   0.289  1.00  1.00
ATOM      9  CA  ALA     1      -0.062   0.001   0.310  1.00  1.00
ATOM     10  HA  ALA     1      -0.008  -1.054   0.497  1.00  1.00
ATOM     11  CB  ALA     1       0.131   0.162  -1.216  1.00  1.00
ATOM     15  CRP ALA     1       1.142   0.546   1.099  1.00  1.00
ATOM     16  OR  ALA     1       1.741  -0.171   1.894  1.00  1.00
ATOM     17  NR  ALA     1       1.537   1.815   0.864  1.00  1.00
ATOM     18  HR  ALA     1       0.963   2.391   0.297  1.00  1.00
ATOM     19  CR  ALA     1       2.669   2.426   1.513  1.00  1.00
END
REMARK X=33 Y=34 
ATOM      1  CL  ALA     1      -3.321   1.436   1.650  1.00  1.00
ATOM      5  CLP ALA     1      -1.870   1.422   1.372  1.00  1.00
ATOM      6  OL  ALA     1      -1.182   2.323   1.789  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.347   0.697  1.00  1.00
ATOM      8  HL  ALA     1      -2.106  -0.263   0.374  1.00  1.00
ATOM      9  CA  ALA     1      -0.057   0.008   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.002  -1.051   0.446  1.00  1.00
ATOM     11  CB  ALA     1       0.113   0.213  -1.212  1.00  1.00
ATOM     15  CRP ALA     1       1.139   0.538   1.102  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.196   1.881  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.803   0.879  1.00  1.00
ATOM     18  HR  ALA     1       0.972   2.397   0.326  1.00  1.00
ATOM     19  CR  ALA     1       2.672   2.407   1.539  1.00  1.00
END
REMARK X=34 Y=35 
ATOM      1  CL  ALA     1      -3.318   1.434   1.657  1.00  1.00
ATOM      5  CLP ALA     1      -1.871   1.426   1.363  1.00  1.00
ATOM      6  OL  ALA     1      -1.186   2.341   1.756  1.00  1.00
ATOM      7  NL  ALA     1      -1.422   0.343   0.704  1.00  1.00
ATOM      8  HL  ALA     1      -2.101  -0.279   0.398  1.00  1.00
ATOM      9  CA  ALA     1      -0.058   0.010   0.290  1.00  1.00
ATOM     10  HA  ALA     1       0.005  -1.051   0.433  1.00  1.00
ATOM     11  CB  ALA     1       0.109   0.227  -1.215  1.00  1.00
ATOM     15  CRP ALA     1       1.138   0.536   1.100  1.00  1.00
ATOM     16  OR  ALA     1       1.723  -0.202   1.878  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.802   0.887  1.00  1.00
ATOM     18  HR  ALA     1       0.970   2.398   0.335  1.00  1.00
ATOM     19  CR  ALA     1       2.675   2.402   1.547  1.00  1.00
END
REMARK X=35 Y=36 
ATOM      1  CL  ALA     1      -3.297   1.417   1.700  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.437   1.310  1.00  1.00
ATOM      6  OL  ALA     1      -1.214   2.432   1.560  1.00  1.00
ATOM      7  NL  ALA     1      -1.412   0.320   0.746  1.00  1.00
ATOM      8  HL  ALA     1      -2.060  -0.372   0.544  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.025   0.282  1.00  1.00
ATOM     10  HA  ALA     1       0.023  -1.051   0.357  1.00  1.00
ATOM     11  CB  ALA     1       0.071   0.308  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.141   0.510   1.103  1.00  1.00
ATOM     16  OR  ALA     1       1.724  -0.245   1.863  1.00  1.00
ATOM     17  NR  ALA     1       1.541   1.794   0.938  1.00  1.00
ATOM     18  HR  ALA     1       0.957   2.397   0.401  1.00  1.00
ATOM     19  CR  ALA     1       2.683   2.371   1.604  1.00  1.00
END
REMARK X=36 Y=37 
ATOM      1  CL  ALA     1      -3.283   1.421   1.730  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.449   1.277  1.00  1.00
ATOM      6  OL  ALA     1      -1.222   2.476   1.436  1.00  1.00
ATOM      7  NL  ALA     1      -1.405   0.299   0.773  1.00  1.00
ATOM      8  HL  ALA     1      -2.034  -0.422   0.640  1.00  1.00
ATOM      9  CA  ALA     1      -0.063   0.028   0.272  1.00  1.00
ATOM     10  HA  ALA     1       0.015  -1.050   0.307  1.00  1.00
ATOM     11  CB  ALA     1       0.057   0.364  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.134   0.492   1.093  1.00  1.00
ATOM     16  OR  ALA     1       1.729  -0.288   1.825  1.00  1.00
ATOM     17  NR  ALA     1       1.539   1.779   0.976  1.00  1.00
ATOM     18  HR  ALA     1       0.945   2.388   0.456  1.00  1.00
ATOM     19  CR  ALA     1       2.682   2.335   1.653  1.00  1.00
END
REMARK X=37 Y=38 
ATOM      1  CL  ALA     1      -3.265   1.435   1.760  1.00  1.00
ATOM      5  CLP ALA     1      -1.868   1.457   1.257  1.00  1.00
ATOM      6  OL  ALA     1      -1.229   2.500   1.343  1.00  1.00
ATOM      7  NL  ALA     1      -1.398   0.292   0.802  1.00  1.00
ATOM      8  HL  ALA     1      -2.014  -0.454   0.728  1.00  1.00
ATOM      9  CA  ALA     1      -0.067   0.024   0.264  1.00  1.00
ATOM     10  HA  ALA     1       0.011  -1.049   0.257  1.00  1.00
ATOM     11  CB  ALA     1       0.028   0.426  -1.206  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.464   1.092  1.00  1.00
ATOM     16  OR  ALA     1       1.748  -0.346   1.781  1.00  1.00
ATOM     17  NR  ALA     1       1.532   1.754   1.029  1.00  1.00
ATOM     18  HR  ALA     1       0.931   2.385   0.536  1.00  1.00
ATOM     19  CR  ALA     1       2.676   2.280   1.721  1.00  1.00
END
REMARK X=38 Y=39 
ATOM      1  CL  ALA     1      -3.236   1.453   1.772  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.473   1.217  1.00  1.00
ATOM      6  OL  ALA     1      -1.244   2.522   1.222  1.00  1.00
ATOM      7  NL  ALA     1      -1.388   0.292   0.824  1.00  1.00
ATOM      8  HL  ALA     1      -1.982  -0.485   0.827  1.00  1.00
ATOM      9  CA  ALA     1      -0.066   0.031   0.248  1.00  1.00
ATOM     10  HA  ALA     1       0.018  -1.048   0.230  1.00  1.00
ATOM     11  CB  ALA     1       0.011   0.464  -1.213  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.452   1.088  1.00  1.00
ATOM     16  OR  ALA     1       1.767  -0.373   1.737  1.00  1.00
ATOM     17  NR  ALA     1       1.517   1.749   1.061  1.00  1.00
ATOM     18  HR  ALA     1       0.906   2.387   0.586  1.00  1.00
ATOM     19  CR  ALA     1       2.660   2.262   1.754  1.00  1.00
END
REMARK X=39 Y=40 
ATOM      1  CL  ALA     1      -3.225   1.461   1.784  1.00  1.00
ATOM      5  CLP ALA     1      -1.878   1.466   1.191  1.00  1.00
ATOM      6  OL  ALA     1      -1.276   2.527   1.106  1.00  1.00
ATOM      7  NL  ALA     1      -1.375   0.274   0.839  1.00  1.00
ATOM      8  HL  ALA     1      -1.947  -0.517   0.921  1.00  1.00
ATOM      9  CA  ALA     1      -0.077   0.024   0.236  1.00  1.00
ATOM     10  HA  ALA     1       0.009  -1.048   0.194  1.00  1.00
ATOM     11  CB  ALA     1      -0.004   0.503  -1.214  1.00  1.00
ATOM     15  CRP ALA     1       1.144   0.436   1.066  1.00  1.00
ATOM     16  OR  ALA     1       1.800  -0.403   1.678  1.00  1.00
ATOM     17  NR  ALA     1       1.483   1.736   1.091  1.00  1.00
ATOM     18  HR  ALA     1       0.861   2.388   0.647  1.00  1.00
ATOM     19  CR  ALA     1       2.642   2.246   1.792  1.00  1.00
END
REMARK X=40 Y=41 
ATOM      1  CL  ALA     1      -3.212   1.465   1.797  1.00  1.00
ATOM      5  CLP ALA     1      -1.874   1.470   1.168  1.00  1.00
ATOM      6  OL  ALA     1      -1.286   2.526   1.008  1.00  1.00
ATOM      7  NL  ALA     1      -1.363   0.265   0.860  1.00  1.00
ATOM      8  HL  ALA     1      -1.914  -0.534   1.016  1.00  1.00
ATOM      9  CA  ALA     1      -0.074   0.012   0.232  1.00  1.00
ATOM     10  HA  ALA     1       0.001  -1.058   0.173  1.00  1.00
ATOM     11  CB  ALA     1      -0.020   0.528  -1.210  1.00  1.00
ATOM     15  CRP ALA     1       1.147   0.408   1.060  1.00  1.00
ATOM     16  OR  ALA     1       1.827  -0.445   1.625  1.00  1.00
ATOM     17  NR  ALA     1       1.461   1.721   1.140  1.00  1.00
ATOM     18  HR  ALA     1       0.821   2.361   0.731  1.00  1.00
ATOM     19  CR  ALA     1       2.614   2.214   1.845  1.00  1.00
END
REMARK X=41 Y=42 
ATOM      1  CL  ALA     1      -3.185   1.487   1.790  1.00  1.00
ATOM      5  CLP ALA     1      -1.865   1.480   1.139  1.00  1.00
ATOM      6  OL  ALA     1      -1.293   2.532   0.896  1.00  1.00
ATOM      7  NL  ALA     1      -1.349   0.268   0.862  1.00  1.00
ATOM      8  HL  ALA     1      -1.881  -0.527   1.095  1.00  1.00
ATOM      9  CA  ALA     1      -0.065   0.013   0.226  1.00  1.00
ATOM     10  HA  ALA     1      -0.006  -1.063   0.151  1.00  1.00
ATOM     11  CB  ALA     1      -0.019   0.539  -1.224  1.00  1.00
ATOM     15  CRP ALA     1       1.170   0.398   1.031  1.00  1.00
ATOM     16  OR  ALA     1       1.871  -0.463   1.540  1.00  1.00
ATOM     17  NR  ALA     1       1.447   1.706   1.159  1.00  1.00
ATOM     18  HR  ALA     1       0.788   2.362   0.800  1.00  1.00
ATOM     19  CR  ALA     1       2.602   2.205   1.868  1.00  1.00
END
REMARK X=42 Y=43 
ATOM      1  CL  ALA     1      -3.257   1.605   1.105  1.00  1.00
ATOM      5  CLP ALA     1      -1.941   1.459   0.447  1.00  1.00
ATOM      6  OL  ALA     1      -1.481   2.369  -0.223  1.00  1.00
ATOM      7  NL  ALA     1      -1.303   0.291   0.647  1.00  1.00
ATOM      8  HL  ALA     1      -1.743  -0.379   1.229  1.00  1.00
ATOM      9  CA  ALA     1      -0.011  -0.077   0.099  1.00  1.00
ATOM     10  HA  ALA     1       0.155  -1.099   0.417  1.00  1.00
ATOM     11  CB  ALA     1       0.001  -0.097  -1.439  1.00  1.00
ATOM     15  CRP ALA     1       1.191   0.673   0.683  1.00  1.00
ATOM     16  OR  ALA     1       2.015   0.103   1.375  1.00  1.00
ATOM     17  NR  ALA     1       1.303   1.983   0.393  1.00  1.00
ATOM     18  HR  ALA     1       0.553   2.411  -0.109  1.00  1.00
ATOM     19  CR  ALA     1       2.395   2.811   0.843  1.00  1.00
END
FIXED
  
  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
# PLUMED interprets the command:
# Y: PDB2CONSTANT ARG=Y NOARGS REFERENCE=regtest/trajectories/path_msd/allv.pdb
# as follows (Click the red comment above to revert to the short version of the input):
YThe CONSTANT action with label Y calculates the following quantities:
 Quantity   
 Type   
 Description  
Y
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43
# --- End of included input --- 
# Generate the projection of the instantaneous coordinates
projThe PROJECT_POINTS action with label proj calculates the following quantities:
 Quantity   
 Type   
 Description  
proj.coord-1
scalar
the coordinates of the points in the low dimensional space  This is the 1th of these quantities
proj.coord-2
scalar
the coordinates of the points in the low dimensional space  This is the 2th of these quantities: PROJECT_POINTSFind the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input This action has hidden defaults. More details ARGthe projections of the landmark points=X,Y TARGET1the matrix of target quantities that you would like to match=rmsd WEIGHTS1the matrix with the weights of the target quantities=weights
proj: PROJECT_POINTSFind the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input This action uses the defaults shown here. More details ARGthe projections of the landmark points=X,Y TARGET1the matrix of target quantities that you would like to match=rmsd WEIGHTS1the matrix with the weights of the target quantities=weights  CGTOL the tolerance for the conjugate gradient minimization=1E-6

# And output the projection to a file
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=proj.* FILEthe name of the file on which to output these quantities=colvar

For ths input there are 42 landmark points and dissimilarities are computed by computing the RMSD distance between the 13 atoms in each of landmark coordinates and the instaneous positions of those 13 atoms.

Using transformed distances

In SKETCHMAP the stress function that is minimised is not the one given above. Instead of seeking to generate a projection, $y_\textrm{min}$, which is at a point where the distances between it and each projection the landmarks is the same as the dissimilarities between the high-dimensional coordinate of the point and the high-dimensional landmarks, the dissimilarities and distances are transformed by functions as illustrated below:

$$\chi(y) = \sum_{i=1}^N w_i [ F[D(X_i, Y)] - f[d(x_i,y)] ]^2$$

The two functions $F$ and $f$ in this expression are usually different as you can see in the input below:

Click on the labels of the actions for more information on what each action computes

# The coordinates of the landmarks in the high dimensional space
d1_refThe CONSTANT action with label d1_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
d1_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1.0,2.0,1.5,2.1
d1_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1.0,2.0,1.5,2.1  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
d2_refThe CONSTANT action with label d2_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
d2_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.5,0.7,0.2,1.3
d2_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.5,0.7,0.2,1.3  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
d3_refThe CONSTANT action with label d3_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
d3_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=3.1,2.0,1.5,0.5
d3_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=3.1,2.0,1.5,0.5  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0

# The weights of the landmark
weightsThe CONSTANT action with label weights calculates the following quantities:
 Quantity   
 Type   
 Description  
weights
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1,1,1,1
weights: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1,1,1,1  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0

# The projections of the landmarks in the low dimensional space
proj1_refThe CONSTANT action with label proj1_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
proj1_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.5,0.8,0.2,0.4
proj1_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.5,0.8,0.2,0.4  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
proj2_refThe CONSTANT action with label proj2_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
proj2_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.2,0.9,0.3,0.7
proj2_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.2,0.9,0.3,0.7  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0

# Calcuate the instantaneous values of the distances
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1,2 ATOMS2the pair of atom that we are calculating the distance between=7,8   ATOMS3the pair of atom that we are calculating the distance between=13,14 ATOMS4the pair of atom that we are calculating the distance between=19,20
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=3,4 ATOMS2the pair of atom that we are calculating the distance between=9,10  ATOMS3the pair of atom that we are calculating the distance between=15,16 ATOMS4the pair of atom that we are calculating the distance between=21,22
d3The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=5,6 ATOMS2the pair of atom that we are calculating the distance between=11,12 ATOMS3the pair of atom that we are calculating the distance between=17,18 ATOMS4the pair of atom that we are calculating the distance between=23,24

# Calculate the distances between the instananeous points and the current positions
edThe EUCLIDEAN_DISTANCE action with label ed calculates the following quantities:
 Quantity   
 Type   
 Description  
ed
vector
the euclidean distances between the input vectors: EUCLIDEAN_DISTANCECalculate the euclidean distance between two vectors of arguments This action is a shortcut. More details SQUARED The squared distance should be calculated ARG1The poin that we are calculating the distance from=d1,d2,d3 ARG2The point that we are calculating the distance to=d1_ref,d2_ref,d3_ref
# PLUMED interprets the command:
# ed: EUCLIDEAN_DISTANCE SQUARED ARG1=d1,d2,d3 ARG2=d1_ref,d2_ref,d3_ref
# as follows (Click the red comment above to revert to the short version of the input):
ed_diffThe VSTACK action with label ed_diff calculates the following quantities:
 Quantity   
 Type   
 Description  
ed_diff
matrix
a matrix that contains the input vectors in its columns: DISPLACEMENTCalculate the displacement vector between the pair of input vectors More details ARG1The point that we are calculating the distance from=d1,d2,d3 ARG2The point that we are calculating the distance to=d1_ref,d2_ref,d3_ref
ed_diffTThe TRANSPOSE action with label ed_diffT calculates the following quantities:
 Quantity   
 Type   
 Description  
ed_diffT
matrix
the transpose of the input matrix: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=ed_diff
edThe MATRIX_PRODUCT_DIAGONAL action with label ed calculates the following quantities:
 Quantity   
 Type   
 Description  
ed
vector
a vector containing the diagonal elements of the matrix that obtaned by multiplying the two input matrices together: MATRIX_PRODUCT_DIAGONALCalculate the product of two matrices and return a vector that contains the diagonal elements of the ouptut vector More details ARGthe two vectors/matrices whose product are to be taken=ed_diff,ed_diffT
# --- End of included input --- 
# Transform the dissimilarities by applying the funciton F
fedThe MORE_THAN action with label fed calculates the following quantities:
 Quantity   
 Type   
 Description  
fed
vector
the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=ed SQUARED is the input quantity the square of the value that you would like to apply the switching function to SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={SMAP R_0=4 A=3 B=2}

# And generate the projection
projThe PROJECT_POINTS action with label proj calculates the following quantities:
 Quantity   
 Type   
 Description  
proj.coord-1
scalar
the coordinates of the points in the low dimensional space  This is the 1th of these quantities
proj.coord-2
scalar
the coordinates of the points in the low dimensional space  This is the 2th of these quantities: PROJECT_POINTSFind the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input This action has hidden defaults. More details ARGthe projections of the landmark points=proj1_ref,proj2_ref TARGET1the matrix of target quantities that you would like to match=fed FUNC1a function that is applied on the distances between the points in the low dimensional space={SMAP R_0=4 A=1 B=2} WEIGHTS1the matrix with the weights of the target quantities=weights
proj: PROJECT_POINTSFind the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input This action uses the defaults shown here. More details ARGthe projections of the landmark points=proj1_ref,proj2_ref TARGET1the matrix of target quantities that you would like to match=fed FUNC1a function that is applied on the distances between the points in the low dimensional space={SMAP R_0=4 A=1 B=2} WEIGHTS1the matrix with the weights of the target quantities=weights  CGTOL the tolerance for the conjugate gradient minimization=1E-6

# And output the projection to a file
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=proj.* FILEthe name of the file on which to output these quantities=colvar

In the input above the function, $F$, that is applied on the dissimilarities is implemented using a MORE_THAN action. The function, $f$, that is applied on the distances in the low-dimensional space is specified using the FUNC keyword that is input to PROJECT_POINTS.

Using multiple targets

At its most complex this action allows you to minimise a stress function such as the one below:

$$\chi(y) = \sum_{i=1}^N \sum_{j=1}^M w_{ij} [ F_j[D(X_i, Y)] - f_j[d(x_i,y)] ]^2$$

The input below shows how this can be implemted within PLUMED:

Click on the labels of the actions for more information on what each action computes

# The coordinates of the landmarks in the high dimensional space
d1_refThe CONSTANT action with label d1_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
d1_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1.0,2.0,1.5,2.1
d1_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1.0,2.0,1.5,2.1  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
d2_refThe CONSTANT action with label d2_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
d2_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.5,0.7,0.2,1.3
d2_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.5,0.7,0.2,1.3  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
d3_refThe CONSTANT action with label d3_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
d3_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=3.1,2.0,1.5,0.5
d3_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=3.1,2.0,1.5,0.5  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0

# The weights of the landmark
weightsThe CONSTANT action with label weights calculates the following quantities:
 Quantity   
 Type   
 Description  
weights
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1,1,1,1
weights: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1,1,1,1  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
w1The CUSTOM action with label w1 calculates the following quantities:
 Quantity   
 Type   
 Description  
w1
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=weights FUNCthe function you wish to evaluate=0.3*x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
w2The CUSTOM action with label w2 calculates the following quantities:
 Quantity   
 Type   
 Description  
w2
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=weights FUNCthe function you wish to evaluate=(1-0.3)*x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# The projections of the landmarks in the low dimensional space
proj1_refThe CONSTANT action with label proj1_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
proj1_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.5,0.8,0.2,0.4
proj1_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.5,0.8,0.2,0.4  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
proj2_refThe CONSTANT action with label proj2_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
proj2_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.2,0.9,0.3,0.7
proj2_ref: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.2,0.9,0.3,0.7  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0

# Calcuate the instantaneous values of the distances
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1,2 ATOMS2the pair of atom that we are calculating the distance between=7,8   ATOMS3the pair of atom that we are calculating the distance between=13,14 ATOMS4the pair of atom that we are calculating the distance between=19,20
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=3,4 ATOMS2the pair of atom that we are calculating the distance between=9,10  ATOMS3the pair of atom that we are calculating the distance between=15,16 ATOMS4the pair of atom that we are calculating the distance between=21,22
d3The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=5,6 ATOMS2the pair of atom that we are calculating the distance between=11,12 ATOMS3the pair of atom that we are calculating the distance between=17,18 ATOMS4the pair of atom that we are calculating the distance between=23,24

# Calculate the distances between the instananeous points and the current positions
edThe EUCLIDEAN_DISTANCE action with label ed calculates the following quantities:
 Quantity   
 Type   
 Description  
ed
vector
the euclidean distances between the input vectors: EUCLIDEAN_DISTANCECalculate the euclidean distance between two vectors of arguments This action is a shortcut. More details SQUARED The squared distance should be calculated ARG1The poin that we are calculating the distance from=d1,d2,d3 ARG2The point that we are calculating the distance to=d1_ref,d2_ref,d3_ref
# PLUMED interprets the command:
# ed: EUCLIDEAN_DISTANCE SQUARED ARG1=d1,d2,d3 ARG2=d1_ref,d2_ref,d3_ref
# as follows (Click the red comment above to revert to the short version of the input):
ed_diffThe VSTACK action with label ed_diff calculates the following quantities:
 Quantity   
 Type   
 Description  
ed_diff
matrix
a matrix that contains the input vectors in its columns: DISPLACEMENTCalculate the displacement vector between the pair of input vectors More details ARG1The point that we are calculating the distance from=d1,d2,d3 ARG2The point that we are calculating the distance to=d1_ref,d2_ref,d3_ref
ed_diffTThe TRANSPOSE action with label ed_diffT calculates the following quantities:
 Quantity   
 Type   
 Description  
ed_diffT
matrix
the transpose of the input matrix: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=ed_diff
edThe MATRIX_PRODUCT_DIAGONAL action with label ed calculates the following quantities:
 Quantity   
 Type   
 Description  
ed
vector
a vector containing the diagonal elements of the matrix that obtaned by multiplying the two input matrices together: MATRIX_PRODUCT_DIAGONALCalculate the product of two matrices and return a vector that contains the diagonal elements of the ouptut vector More details ARGthe two vectors/matrices whose product are to be taken=ed_diff,ed_diffT
# --- End of included input --- # Transform the dissimilarities by applying the funciton F
fedThe MORE_THAN action with label fed calculates the following quantities:
 Quantity   
 Type   
 Description  
fed
vector
the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=ed SQUARED is the input quantity the square of the value that you would like to apply the switching function to SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={SMAP R_0=4 A=3 B=2}

# And generate the projection
projThe PROJECT_POINTS action with label proj calculates the following quantities:
 Quantity   
 Type   
 Description  
proj.coord-1
scalar
the coordinates of the points in the low dimensional space  This is the 1th of these quantities
proj.coord-2
scalar
the coordinates of the points in the low dimensional space  This is the 2th of these quantities: PROJECT_POINTSFind the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input This action has hidden defaults. More details ...
  ARGthe projections of the landmark points=proj1_ref,proj2_ref
  TARGET1the matrix of target quantities that you would like to match=ed WEIGHTS1the matrix with the weights of the target quantities=w1 FUNC1a function that is applied on the distances between the points in the low dimensional space={CUSTOM FUNC=1-sqrt(x2) R_0=1.0}
  TARGET2the matrix of target quantities that you would like to match=fed WEIGHTS2the matrix with the weights of the target quantities=w2 FUNC2a function that is applied on the distances between the points in the low dimensional space={SMAP R_0=4 A=1 B=2}
...
proj: PROJECT_POINTSFind the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input This action uses the defaults shown here. More details ...
  ARGthe projections of the landmark points=proj1_ref,proj2_ref
  TARGET1the matrix of target quantities that you would like to match=ed WEIGHTS1the matrix with the weights of the target quantities=w1 FUNC1a function that is applied on the distances between the points in the low dimensional space={CUSTOM FUNC=1-sqrt(x2) R_0=1.0}
  TARGET2the matrix of target quantities that you would like to match=fed WEIGHTS2the matrix with the weights of the target quantities=w2 FUNC2a function that is applied on the distances between the points in the low dimensional space={SMAP R_0=4 A=1 B=2}
 CGTOL the tolerance for the conjugate gradient minimization=1E-6
...

# And output the projection to a file
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=proj.* FILEthe name of the file on which to output these quantities=colvar

Here the sum over $M$ in the expression above has two terms. In the first of these terms $F_1$ is the identity so the input for TARGET1 is the output from EUCLIDEAN_DISTANCE. $f_1$ is similarly the identity. To implement the identity here we use the input to FUNC1 shown above. The input to this function is the input for one of the switching functions described in the documentation for LESS_THAN. What we compute for the transformed distance is $1-s(d)$ where $s(d)$ is the switching function that is specified in input. Consequently, applying the function 1-sqrt(x2) returns the distance.

The second term in our sum over $M$ in the input above has the dissimilarities and distances transformed by the functions that we introduced in the previous section.

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
ARG	vector	the projections of the landmark points
TARGET	vector/matrix	the matrix of target quantities that you would like to match
WEIGHTS	vector	the matrix with the weights of the target quantities

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ARG	input	none	the projections of the landmark points
TARGET	input	none	the matrix of target quantities that you would like to match
WEIGHTS	input	none	the matrix with the weights of the target quantities
CGTOL	compulsory	1E-6	the tolerance for the conjugate gradient minimization
FUNC	optional	not used	a function that is applied on the distances between the points in the low dimensional space
SERIAL	optional	false	do the calculation in serial. Further information about this flag can be found here.
USEGPU	optional	false	run this calculation on the GPU. Further information about this flag can be found here.