Tool Set Documentation

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usage: [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]
          [-custom file]

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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.


usage information
-prefix name 
prefix for output files
generate CHARMM log files at each stage
generate trajectory files at each stage
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
fix solute atoms
-densitysteps value 
number of time steps during simulation for estimating solent density
-equi temp:steps[=temp:steps ...] 
heating protocol
solvate in cubic box
solvate in ocatahedron
-cutoff value 
minimum distance from solute to edge of solvation box
add counterions to neutralize system
-addions concentraion 
add NaCl ion pairs to reach given concentration
-custom file 
provide custom CHARMM input file
provide extensive information about progress of equilibration