equiCHARMM.pl

Usage

usage:    equiCHARMM.pl [options] PDBfile
options:  [-prefix filename] [-logs] [-trajs] [-cmds]
          [-par CHARMMparams]
          [-cons [ca|cb|cab|heavy] refpdb|self min:max[_force][=...]]
          [-fixsolute] [-densitysteps value]
          [-equi temp:steps[=temp:steps]]
          [-cubicbox] [-octabox] [-cutoff value]
          [-neutralize] [-addions concentration]
          [-[no]center]
          [-custom file]
          [-verbose]

Show source

Description

This script will automatically setup, heatup, and equilibrate a given solute in explicit solvent. The final structure is meant to serve as a starting structure for production moelcular dynamics runs.

Options

-help 

usage information

-prefix name 

prefix for output files

-logs 

generate CHARMM log files at each stage

-trajs 

generate trajectory files at each stage

-cmds 

generate CHARMM input files at each stage

-par key=value[,...] 

CHARMM parameters

-l [ca|cb|cab|heavy] force refpdb|self min:max[=...] 

apply restraints to atoms outside specified residue range

-cons [ca|cb|cab|heavy] refpdb|self min:max[_force][=...] 

apply restraints to specified residue range

-fixsolute 

fix solute atoms

-densitysteps value 

number of time steps during simulation for estimating solent density

-equi temp:steps[=temp:steps ...] 

heating protocol

-cubicbox 

solvate in cubic box

-octabox 

solvate in ocatahedron

-cutoff value 

minimum distance from solute to edge of solvation box

-neutralize 

add counterions to neutralize system

-addions concentraion 

add NaCl ion pairs to reach given concentration

-custom file 

provide custom CHARMM input file

-verbose 

provide extensive information about progress of equilibration