MMTSB
Tool Set Documentation

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>
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  <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
 +
 
 +
 
 +
== 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>

Revision as of 22:49, 7 January 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]
Show source


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


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

...