PARABETARMSD

This is part of the secondarystructure module |

Probe the parallel beta sheet content of your protein structure.

Two protein segments containing three contiguous residues can form a parallel beta sheet. Although if the two segments are part of the same protein chain they must be separated by a minimum of 3 residues to make room for the turn. This colvar thus generates the set of all possible six residue sections that could conceivably form a parallel beta sheet and calculates the RMSD distance between the configuration in which the residues find themselves and an idealized parallel beta sheet structure. These distances can be calculated by either aligning the instantaneous structure with the reference structure and measuring each atomic displacement or by calculating differences between the set of inter-atomic distances in the reference and instantaneous structures.

This colvar is based on the following reference [93]. The authors of this paper use the set of distances from the parallel beta sheet configurations to measure the number of segments whose configuration resembles a parallel beta sheet. This is done by calculating the following sum of functions of the rmsd distances:

\[ s = \sum_i \frac{ 1 - \left(\frac{r_i-d_0}{r_0}\right)^n } { 1 - \left(\frac{r_i-d_0}{r_0}\right)^m } \]

where the sum runs over all possible segments of parallel beta sheet. By default the NN, MM and D_0 parameters are set equal to those used in [93]. The R_0 parameter must be set by the user - the value used in [93] was 0.08 nm.

If you change the function in the above sum you can calculate quantities such as the average distance from a structure composed of only parallel beta sheets or the distance between the set of residues that is closest to a parallel beta sheet and the reference configuration. To do these sorts of calculations you can use the AVERAGE and MIN keywords. In addition you can use the LESS_THAN keyword if you would like to change the form of the switching function. If you use any of these options you no longer need to specify NN, R_0, MM and D_0.

Please be aware that for codes like gromacs you must ensure that plumed reconstructs the chains involved in your CV when you calculate this CV using anything other than TYPE=DRMSD. For more details as to how to do this see WHOLEMOLECULES.

- Examples

The following input calculates the number of six residue segments of protein that are in an parallel beta sheet configuration.

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

#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb MOLINFOSTRUCTURE=beta.pdbcompulsory keyworda file in pdb format containing a reference structure.pb:PARABETARMSDRESIDUES=allthis command is used to specify the set of residues that could conceivably form part of the secondary structure.STRANDS_CUTOFF=1If in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like.

Here the same is done use RMSD instead of DRMSD

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

#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb MOLINFOSTRUCTURE=helix.pdb WHOLEMOLECULEScompulsory keyworda file in pdb format containing a reference structure.ENTITY0=1-100the atoms that make up a molecule that you wish to align.hh:PARABETARMSDRESIDUES=allthis command is used to specify the set of residues that could conceivably form part of the secondary structure.TYPE=OPTIMALcompulsory keyword ( default=DRMSD )the manner in which RMSD alignment is performed.R_0=0.1could not find this keywordSTRANDS_CUTOFF=1If in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like.

- Glossary of keywords and components

- Description of components

By default this Action calculates the number of structural units that are within a certain distance of a idealized secondary structure element. This quantity can then be referenced elsewhere in the input by using the label of the action. However, this Action can also be used to calculate the following quantities by using the keywords as described below. The quantities then calculated can be referenced using the label of the action followed by a dot and then the name from the table below. Please note that you can use the LESS_THAN keyword more than once. The resulting components will be labelled *label*.lessthan-1, *label*.lessthan-2 and so on unless you exploit the fact that these labels can be given custom labels by using the LABEL keyword in the description of you LESS_THAN function that you are computing

Quantity | Keyword | Description |

altmin | ALT_MIN | the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous. |

highest | HIGHEST | the highest of the quantities calculated by this action |

lessthan | LESS_THAN | the number of values less than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters. |

lowest | LOWEST | the lowest of the quantities calculated by this action |

min | MIN | the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous. |

- The atoms involved can be specified using

RESIDUES | this command is used to specify the set of residues that could conceivably form part of the secondary structure. It is possible to use residues numbers as the various chains and residues should have been identified else using an instance of the MOLINFO action. If you wish to use all the residues from all the chains in your system you can do so by specifying all. Alternatively, if you wish to use a subset of the residues you can specify the particular residues you are interested in as a list of numbers. Please be aware that to form secondary structure elements your chain must contain at least N residues, where N is dependent on the particular secondary structure you are interested in. As such if you define portions of the chain with fewer than N residues the code will crash. |

- Compulsory keywords

TYPE | ( default=DRMSD ) the manner in which RMSD alignment is performed. Should be OPTIMAL, SIMPLE or DRMSD. For more details on the OPTIMAL and SIMPLE methods see RMSD. For more details on the DRMSD method see DRMSD. |

R_0 | ( default=0.08 ) The r_0 parameter of the switching function. |

D_0 | ( default=0.0 ) The d_0 parameter of the switching function |

NN | ( default=8 ) The n parameter of the switching function |

MM | ( default=12 ) The m parameter of the switching function |

STYLE | ( default=all ) Parallel beta sheets can either form in a single chain or from a pair of chains. If STYLE=all all chain configuration with the appropriate geometry are counted. If STYLE=inter only sheet-like configurations involving two chains are counted, while if STYLE=intra only sheet-like configurations involving a single chain are counted |

- Options

NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |

NOPBC | ( default=off ) ignore the periodic boundary conditions |

VERBOSE | ( default=off ) write a more detailed output |

SERIAL | ( default=off ) do the calculation in serial. Do not use MPI |

LOWMEM | ( default=off ) lower the memory requirements |

TIMINGS | ( default=off ) output information on the timings of the various parts of the calculation |

LESS_THAN | calculate the number of variables less than a certain target value. This quantity is calculated using \(\sum_i \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction. The final value can be referenced using label.lessthan. You can use multiple instances of this keyword i.e. LESS_THAN1, LESS_THAN2, LESS_THAN3... The corresponding values are then referenced using label.lessthan-1, label.lessthan-2, label.lessthan-3... |

MIN | calculate the minimum value. To make this quantity continuous the minimum is calculated using \( \textrm{min} = \frac{\beta}{ \log \sum_i \exp\left( \frac{\beta}{s_i} \right) } \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)) The final value can be referenced using label.min. You can use multiple instances of this keyword i.e. MIN1, MIN2, MIN3... The corresponding values are then referenced using label.min-1, label.min-2, label.min-3... |

ALT_MIN | calculate the minimum value. To make this quantity continuous the minimum is calculated using \( \textrm{min} = -\frac{1}{\beta} \log \sum_i \exp\left( -\beta s_i \right) \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)). The final value can be referenced using label.altmin. You can use multiple instances of this keyword i.e. ALT_MIN1, ALT_MIN2, ALT_MIN3... The corresponding values are then referenced using label.altmin-1, label.altmin-2, label.altmin-3... |

LOWEST | this flag allows you to recover the lowest of these variables. The final value can be referenced using label.lowest |

HIGHEST | this flag allows you to recover the highest of these variables. The final value can be referenced using label.highest |

STRANDS_CUTOFF | If in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like. This keyword speeds up the calculation enormously when you are using the LESS_THAN option. However, if you are using some other option, then this cannot be used |