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

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