Difference between revisions of "latticeener.pl"
Revision as of 14:18, 12 August 2006
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]
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 <docmark>genchain.pl</docmark>.
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 <docmark>geninput.pl</docmark>.
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.
- usage information
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