MMTSB
Tool Set Documentation

processDCD.pl

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Usage

usage:    processDCD.pl [template] [dcdfile(s)]
options:  [-inx index[:to]] [-step n]
          [-multi from:to]
          [-apply cmd]
          [-function file]
          [-extract name]
          [-ensdir dir] [-ens tag]
          [-rms CA|CAB|C|O|N|side|back|all ref]
          [-qscore ref] [-boxsize]
          [-wrapseg]
          [-average] [-fit ref] [-fitsel cab|ca|cb|heavy] [-fitresnumonly]
          [-psf file]
          [-atoms from:to]
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Description

Process a CHARMM trajectory file with custom commands and custom functions. This function provides similar function to analyzeCHARMM.pl but does not require CHARMM and offers greater flexibility, especially for non-standard systems.

Options

-help 
usage information
-inx from:to 
analyze the specified frame range from trajectory file
-step size 
skip the specified number of steps in between frame analyses
-multi from:to 
read from multiple DCD files (file name given as template) with indices according to given range of numbers
-apply cmd 
each frame will be temporarily converted into a PDB file and analyzed according to the given command
-function file 
analyze frames with an internal perl function (see analyze.pl for more information
-extract name 
extract structures and store them as PDB files with a common tag name
-ensdir dir 
extract structures into an ensemble with the specified directory name
-ens tag 
extract structures into an ensemble with the specified tag name
-rms CA|CAB|C|O|N|side|back|all ... ref 
calculate the root mean square deviation of each frame with respect to a reference PDB structure
-qscore ref 
calculate Q-score for each frame
-boxsize 
extract box size information from trajectory
-average 
calculate average structure from trajectory
-fit ref 
fit each frame to the reference
-fitsel cab|ca|cb|heavy 
fit each frame with respect to the specified atom selection
-psf file 
use specified protein structure file (PSF)
-atoms from:to 
use specified atom selection range

Examples

processDCD.pl -inx 5:10 -apply rgyr.pl 1vii.pdb 1vii.dcd
calculates the radius of gyration for structures from frames 5-10 from this trajectory

reading from 1vii.dcd
5 5.0000 12.303517
6 6.0000 9.622869
7 7.0000 9.159078
8 8.0000 9.735043
9 9.0000 9.278946
10 10.0000 9.796450