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Difference between revisions of "latticeener.pl"
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given lattice chain without actually running MONSSTER. | given lattice chain without actually running MONSSTER. | ||
The input can be either a sequence and chain file in MONSSTER format | The input can be either a sequence and chain file in MONSSTER format | ||
| − | or a chain PDB file that can be generated with | + | or a chain PDB file that can be generated with [[genchain.pl]].<BR> |
Scaling factors for various energy components in the SICHO energy function | Scaling factors for various energy components in the SICHO energy function | ||
can be specified with <B>-par</B> followed by key=value pairs. A more | can be specified with <B>-par</B> followed by key=value pairs. A more | ||
detailed explanation can be found in the description of | detailed explanation can be found in the description of | ||
| − | + | [[geninput.pl]].<BR> | |
The output consists of the total energy, as well as the individual energy components | 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 | for short-range interactions, pair-wise interactions, a burial term, a burial correction term, and | ||
a centrosymmetric term.<BR> | a centrosymmetric term.<BR> | ||
| − | |||
== Options == | == Options == | ||
; -help : usage information | ; -help : usage information | ||
| − | + | ; -par name=value[,...] : SICHO force field parameters | |
== Examples == | == Examples == | ||
Latest revision as of 02:20, 29 July 2009
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