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 [89]. 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 [89]. The R_0 parameter must be set by the user - the value used in [89] 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
MOLINFO STRUCTUREcompulsory keyword 
a file in pdb format containing a reference structure. 
=beta.pdb The MOLINFO action with label 
pb: PARABETARMSD RESIDUESthis command is used to specify the set of residues that could conceivably form part
of the secondary structure. 
=all STRANDS_CUTOFFIf 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. 
=1 The PARABETARMSD action with label pb calculates a single scalar value

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
MOLINFO STRUCTUREcompulsory keyword 
a file in pdb format containing a reference structure. 
=helix.pdb The MOLINFO action with label 
WHOLEMOLECULES ENTITY0the atoms that make up a molecule that you wish to align. 
=1-100 The WHOLEMOLECULES action with label 
hh: PARABETARMSD RESIDUESthis command is used to specify the set of residues that could conceivably form part
of the secondary structure. 
=all TYPEcompulsory keyword ( default=DRMSD )
the manner in which RMSD alignment is performed. 
=OPTIMAL R_0 could not find this keyword 
=0.1 STRANDS_CUTOFFIf 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. 
=1 The PARABETARMSD action with label hh calculates a single scalar value

Glossary of keywords and components

Description of components

By default this Action calculates the following quantities. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
.#!value	if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet. If LESS_THAN is not present the number of residue segments where the structure is similar to a parallel beta sheet
struct	the vectors containing the rmsd distances between the residues and each of the reference structures
lessthan	the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold

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.
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

SERIAL	( default=off ) do the calculation in serial. Do not parallelize
NOPBC	( default=off ) ignore the periodic boundary conditions
VERBOSE	( default=off ) write a more detailed output
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
LESS_THAN	calculate the number of a residue segments that are within a certain target distance of this secondary structure type. This quantity is calculated using \(\sum_i \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction.
R_0	The r_0 parameter of the switching function.