MMTSB
Tool Set Documentation

latticeener.pl

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Usage

usage:   latticeener.pl [options] [seqFile chainFile | pdbFile]
options: [-par stiff=val,short=val,central=val,kdcore=val,
               softcore=val,pair=val,hbond=val,short=val,
               burial=val,multibody=val,threebody=val,temp=val]
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Description

This script can be used to evaluate the SICHO energy function for a given lattice chain without actually running MONSSTER. The input can be either a sequence and chain file in MONSSTER format or a chain PDB file that can be generated with genchain.pl.
Scaling factors for various energy components in the SICHO energy function can be specified with -par followed by key=value pairs. A more detailed explanation can be found in the description of geninput.pl.
The output consists of the total energy, as well as the individual energy components for short-range interactions, pair-wise interactions, a burial term, a burial correction term, and a centrosymmetric term.

Options

-help 
usage information
-par name=value[,...] 
SICHO force field parameters

Examples

latticeener.pl 1vii.seq 1vii.exp.chain
evaluates the SICHO energy of the given input chain

78.964588 31.031346 46.683241 -0.600000 6.900000 -5.050000


latticeener.pl -par central=0.5,pair=2.0 1vii.seq 1vii.exp.chain
evaluates the SICHO energy function with different scaling factors

72.252088 31.031346 38.720741 -0.600000 6.900000 -3.800000