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Difference between revisions of "geninput.pl"
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− | + | __NOTOC__ | |
+ | == Usage == | ||
+ | |||
+ | <mmtsbToolUsage cmd="geninput.pl"></mmtsbToolUsage> | ||
+ | |||
+ | == Description == | ||
+ | |||
+ | Generates an input file for MONSSTER. | ||
+ | Available parameters and their default values are shown | ||
+ | in the table below. The values can be overwritten by specifying | ||
+ | the parameter name and the new value with <B>-par</B><BR><BR> | ||
+ | <TABLE CELLPADDING=1 CELLSPACING=2> | ||
+ | <TR> | ||
+ | <TD ALIGN=left><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3><B>Key</B></FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3><B>Explanation</B></FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3><B>Default</B></FONT></TD></TR> | ||
+ | <TR><TD></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>random</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>random seed</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>random value</FONT></TD></TR> | ||
+ | <TR><TD></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>ncycle</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>cycles/temp. step</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>20</FONT></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>icycle</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>MC moves/cycle</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>50</FONT></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>tsteps</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>temperature steps</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>10</FONT></TD></TR> | ||
+ | <TR><TD></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>resmin</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>first fragment residue (fixed template)</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>0</FONT></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>resmax</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>last fragment residue (fixed template)</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>0</FONT></TD></TR> | ||
+ | <TR><TD></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>temp</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>temperature range</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>2.5:1.0</FONT></TD></TR> | ||
+ | <TR><TD></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>softcore</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>soft core radius for large residues</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>4.0</FONT></TD></TR> | ||
+ | <TR><TD></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>central</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>centrosymmetric potential scaling</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>0.25</FONT></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>stiff</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>general stiffness potential scaling</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>1.25</FONT></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>pair</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>pair potential scaling</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>1.0</FONT></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>kdcore</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>hydrophobic core potential scaling</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>0.35</FONT></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>hbond</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>H-bond cooperativity potential scaling</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>-0.3</FONT></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>short</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>short range potential scaling</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>0.5</FONT></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>burial</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>burial potential scaling</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>1.0</FONT></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>multibody</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>multi body potential scaling</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>0.5</FONT></TD></TR> | ||
+ | <TR> | ||
+ | <TD><FONT FACE=courier SIZE=3>threebody</FONT></TD> | ||
+ | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>3 body potential scaling</FONT></TD> | ||
+ | <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>0.25</FONT></TD></TR> | ||
+ | </TABLE><BR> | ||
+ | |||
+ | Distance constraints between residues (e.g. if disulfide linkages are known) | ||
+ | may be specified using <B>-d</B> with a force constant and a list of | ||
+ | residue pairs as parameters. A MONSSTER sequence file may be given with | ||
+ | <B>-seq</B> for translating the residue numbering accordingly. | ||
+ | |||
+ | == Options == | ||
+ | |||
+ | ; -help : usage information | ||
+ | ; -d force res1:res2[=...] : residue-residue distance restraints | ||
+ | ; -par name=value[,...] : SICHO force field parameters | ||
+ | ; -seq file : MONSSTER sequence file | ||
+ | |||
+ | == Examples == | ||
+ | |||
+ | <mmtsbToolExample cmd="geninput.pl" set="/apps/mmtsb/bench/geninput.pl-test/test1"></mmtsbToolExample> | ||
+ | |||
+ | <mmtsbToolExample cmd="geninput.pl" set="/apps/mmtsb/bench/geninput.pl-test/test2"></mmtsbToolExample> |
Latest revision as of 02:22, 29 July 2009
Usage
usage: geninput.pl [options] options: [-d force res1:res2[=res1:res2 ...]] [-par random=val,ncycle=val,icycle=val, tsteps=val,resmin=val,resmax=val, temp=first[:last],softcore=val, central=val,stiff=val,pair=val, kdcore=val,hbond=val,short=val, burial=val,multibody=val,threebody=val] [-seq file]
Description
Generates an input file for MONSSTER.
Available parameters and their default values are shown
in the table below. The values can be overwritten by specifying
the parameter name and the new value with -par
Key | Explanation | Default |
random | random seed | random value |
ncycle | cycles/temp. step | 20 |
icycle | MC moves/cycle | 50 |
tsteps | temperature steps | 10 |
resmin | first fragment residue (fixed template) | 0 |
resmax | last fragment residue (fixed template) | 0 |
temp | temperature range | 2.5:1.0 |
softcore | soft core radius for large residues | 4.0 |
central | centrosymmetric potential scaling | 0.25 |
stiff | general stiffness potential scaling | 1.25 |
pair | pair potential scaling | 1.0 |
kdcore | hydrophobic core potential scaling | 0.35 |
hbond | H-bond cooperativity potential scaling | -0.3 |
short | short range potential scaling | 0.5 |
burial | burial potential scaling | 1.0 |
multibody | multi body potential scaling | 0.5 |
threebody | 3 body potential scaling | 0.25 |
Distance constraints between residues (e.g. if disulfide linkages are known) may be specified using -d with a force constant and a list of residue pairs as parameters. A MONSSTER sequence file may be given with -seq for translating the residue numbering accordingly.
Options
- -help
- usage information
- -d force res1:res2[=...]
- residue-residue distance restraints
- -par name=value[,...]
- SICHO force field parameters
- -seq file
- MONSSTER sequence file
Examples
geninput.pl
generates the default MONSSTER input file
520735 20 50 10 0 0 2.50 1.00 4.000 0.250 1.250 1.000 0.350 -0.300 0.500 1.000 0.500 0.250 0 0.0 0 0 0 0
geninput.pl -par ncycle=50,stiff=0.1 -d 5.0 10:34=19:26
generates a MONSSTER input file iwth 50 cycles per time step and a
modified scaling factor for the general stiffness potential term.
In addition sidechain restraints are specified between residues
10 and 34 as well as 19 and 26.
657610 50 50 10 0 0 2.50 1.00 4.000 0.250 0.100 1.000 0.350 -0.300 0.500 1.000 0.500 0.250 2 5.000000 10 34 19 26 0 0 ...