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latticeener.pl
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]
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