MMTSB
Tool Set Documentation

Difference between revisions of "geninput.pl"

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== Description ==
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G62y77 http://groups.google.com/group/SheenaGertrudeGomez-lra/web/actress-gershon.html actress gershon
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/actress-renee.html actress renee
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Generates an input file for MONSSTER.
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/actress-skye.html actress skye
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Available parameters and their default values are shown
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/actuarial.html actuarial
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in the table below. The values can be overwritten by specifying
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/actuator.html actuator
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the parameter name and the new value with <B>-par</B><BR><BR>
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acu.html acu
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<TABLE CELLPADDING=1 CELLSPACING=2>
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acupuncture.html acupuncture
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<TR>
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-auto.html acura auto
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  <TD ALIGN=left><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3><B>Key</B></FONT></TD>
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-car.html acura car
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3><B>Explanation</B></FONT></TD>
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-cars.html acura cars
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3><B>Default</B></FONT></TD></TR>
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-rl.html acura rl
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<TR><TD></TD></TR>
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-rsx.html acura rsx
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<TR>
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-tl-s.html acura tl s
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  <TD><FONT FACE=courier SIZE=3>random</FONT></TD>
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-tl.html acura tl
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>random seed</FONT></TD>
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-toyota.html acura toyota
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>random value</FONT></TD></TR>
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-used.html acura used
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<TR><TD></TD></TR>
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura.html acura
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<TR>
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http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acute-leukemia.html acute leukemia
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  <TD><FONT FACE=courier SIZE=3>ncycle</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>cycles/temp. step</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>20</FONT></TD></TR>
 
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<TR>
 
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  <TD><FONT FACE=courier SIZE=3>icycle</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>MC moves/cycle</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>50</FONT></TD></TR>
 
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<TR>
 
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  <TD><FONT FACE=courier SIZE=3>tsteps</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>temperature steps</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>10</FONT></TD></TR>
 
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<TR><TD></TD></TR>
 
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<TR>
 
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  <TD><FONT FACE=courier SIZE=3>resmin</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>first fragment residue (fixed template)</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>0</FONT></TD></TR>
 
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<TR>
 
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  <TD><FONT FACE=courier SIZE=3>resmax</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>last fragment residue (fixed template)</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>0</FONT></TD></TR>
 
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<TR><TD></TD></TR>
 
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<TR>
 
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  <TD><FONT FACE=courier SIZE=3>temp</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>temperature range</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>2.5:1.0</FONT></TD></TR>
 
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<TR><TD></TD></TR>
 
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<TR>
 
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  <TD><FONT FACE=courier SIZE=3>softcore</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>soft core radius for large residues</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>4.0</FONT></TD></TR>
 
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<TR><TD></TD></TR>
 
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<TR>
 
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  <TD><FONT FACE=courier SIZE=3>central</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>centrosymmetric potential scaling</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>0.25</FONT></TD></TR>
 
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<TR>
 
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  <TD><FONT FACE=courier SIZE=3>stiff</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>general stiffness potential scaling</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>1.25</FONT></TD></TR>
 
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<TR>
 
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  <TD><FONT FACE=courier SIZE=3>pair</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>pair potential scaling</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>1.0</FONT></TD></TR>
 
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<TR>
 
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  <TD><FONT FACE=courier SIZE=3>kdcore</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>hydrophobic core potential scaling</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>0.35</FONT></TD></TR>
 
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<TR>
 
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  <TD><FONT FACE=courier SIZE=3>hbond</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>H-bond cooperativity potential scaling</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>-0.3</FONT></TD></TR>
 
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<TR>
 
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  <TD><FONT FACE=courier SIZE=3>short</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>short range potential scaling</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>0.5</FONT></TD></TR>
 
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<TR>
 
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  <TD><FONT FACE=courier SIZE=3>burial</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>burial potential scaling</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>1.0</FONT></TD></TR>
 
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<TR>
 
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  <TD><FONT FACE=courier SIZE=3>multibody</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>multi body potential scaling</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>0.5</FONT></TD></TR>
 
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<TR>
 
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  <TD><FONT FACE=courier SIZE=3>threebody</FONT></TD>
 
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  <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>3 body potential scaling</FONT></TD>
 
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  <TD ALIGN=center><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>0.25</FONT></TD></TR>
 
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</TABLE><BR>
 
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Distance constraints between residues (e.g. if disulfide linkages are known)
 
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may be specified using <B>-d</B> with a force constant and a list of
 
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residue pairs as parameters. A MONSSTER sequence file may be given with
 
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<B>-seq</B> for translating the residue numbering accordingly.
 
  
 
== Options ==
 
== Options ==

Revision as of 08:43, 24 August 2008

WtqMOr <a href="http://iemanaoguzrm.com/">iemanaoguzrm</a>, [url=http://ceiqmnyjqavs.com/]ceiqmnyjqavs[/url], [link=http://kjilpjtavjth.com/]kjilpjtavjth[/link], http://pqdelhgcdvil.com/

G62y77 http://groups.google.com/group/SheenaGertrudeGomez-lra/web/actress-gershon.html actress gershon http://groups.google.com/group/SheenaGertrudeGomez-lra/web/actress-renee.html actress renee http://groups.google.com/group/SheenaGertrudeGomez-lra/web/actress-skye.html actress skye http://groups.google.com/group/SheenaGertrudeGomez-lra/web/actuarial.html actuarial http://groups.google.com/group/SheenaGertrudeGomez-lra/web/actuator.html actuator http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acu.html acu http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acupuncture.html acupuncture http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-auto.html acura auto http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-car.html acura car http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-cars.html acura cars http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-rl.html acura rl http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-rsx.html acura rsx http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-tl-s.html acura tl s http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-tl.html acura tl http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-toyota.html acura toyota http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura-used.html acura used http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acura.html acura http://groups.google.com/group/SheenaGertrudeGomez-lra/web/acute-leukemia.html acute leukemia

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

...
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