Action: SECONDARY_STRUCTURE_RMSD

Module secondarystructure
Description Usage
Calclulate the distance between segments of a protein and a reference structure of interest used in 1 tutorialsused in 17 eggs
output value type
a vector containing the rmsd distance between each of the residue segments and the reference structure vector

Output components

This action calculates the values in the following table. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name Type Description
struct vector the vectors containing the rmsd distances between the residues and each of the reference structures
lessthan scalar the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold

Input

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

Keyword Type Description
RESIDUES atoms this command is used to specify the set of residues that could conceivably form part of the secondary structure
ATOMS atoms this is the full list of atoms that we are investigating

Further details and examples

Calclulate the distance between segments of a protein and a reference structure of interest

This action is used in the shortcuts ALPHARMSD, ANTIBETARMSD and PARABETARMSD. It calculates a vector of RMSD values between a single reference multiple configurations and the instantaneous positions of various groups of atoms. For example, in the following input we define a single set of reference set of coordinates for 3 atoms.

Click on the labels of the actions for more information on what each action computes
tested on2.11
c1: SECONDARY_STRUCTURE_RMSDCalclulate the distance between segments of a protein and a reference structure of interest More details BONDLENGTHthe length to use for bonds=0.17 STRUCTURE1the reference structure=1,0,0,0,1,0,0,0,1 SEGMENT1this is the lists of atoms in the segment that are being considered=1,2,3 SEGMENT2this is the lists of atoms in the segment that are being considered=4,5,6 SEGMENT3this is the lists of atoms in the segment that are being considered=7,8,9 SEGMENT4this is the lists of atoms in the segment that are being considered=10,11,12 TYPE the manner in which RMSD alignment is performed=OPTIMAL
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=c1 FILEthe name of the file on which to output these quantities=colvar

A four dimensional vector is then returned that contains the RMSD distances between the 4 sets of atoms that were specified using the SEGMENT keywords and the reference coordinates. Notice that you can use multiple instances of the STRUCTURE keyword. In general the the number of vectors output is equal to the number of times the STRUCTURE keyword is used.

References

More information about how this action can be used is available in the following articles: - F. Pietrucci, A. Laio, A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1. Journal of Chemical Theory and Computation. 5, 2197–2201 (2009)

Syntax

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

Keyword Type Default Description
RESIDUES input none this command is used to specify the set of residues that could conceivably form part of the secondary structure
ATOMS input none this is the full list of atoms that we are investigating
BONDLENGTH compulsory none the length to use for bonds
TYPE compulsory DRMSD the manner in which RMSD alignment is performed
D_0 compulsory 0.0 The d_0 parameter of the switching function
NN compulsory 8 The n parameter of the switching function
MM compulsory 12 The m parameter of the switching function
SERIAL optional false do the calculation in serial
NOPBC optional false ignore the periodic boundary conditions
SEGMENT optional not used this is the lists of atoms in the segment that are being considered
STRUCTURE optional not used the reference structure
STRANDS_CUTOFF optional not used 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
CUTOFF_ATOMS optional not used the pair of atoms that are used to calculate the strand cutoff
VERBOSE optional false write a more detailed output
LESS_THAN optional not used calculate the number of a residue segments that are within a certain target distance of this secondary structure type. Options for this keyword are explained in the documentation for LESS_THAN.
R_0 optional not used The r_0 parameter of the switching function