MMTSB
Tool Set Documentation

Difference between revisions of "mdAmber.pl"

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This script is used to run molecular dynamics with Amber in a similar
 
This script is used to run molecular dynamics with Amber in a similar
way as with <docmark>mdCHARMM.pl</docmark> which uses CHARMM instead.
+
way as with [[mdCHARMM.pl]] which uses CHARMM instead.
The options are very similar to <docmark>minAmber.pl</docmark>.
+
The options are very similar to [[minAmber.pl]].
 
At this point the focus is on running implicit solvent dynamics.
 
At this point the focus is on running implicit solvent dynamics.
 
Explicit water simulations are not supported yet but this
 
Explicit water simulations are not supported yet but this
feature will be added in the near future.<BR><BR>
+
feature will be added in the near future.<BR>
  
 
Output file names can be set with the following options: <B>-final</B>
 
Output file names can be set with the following options: <B>-final</B>
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is read in at the beginning if given with <B>-restart</B>. No Amber parameter
 
is read in at the beginning if given with <B>-restart</B>. No Amber parameter
 
file needs to be generated prior to using this utility, but if an appropriate
 
file needs to be generated prior to using this utility, but if an appropriate
parameter/topology file is available it may be given with <B>-partop</B>.<BR><BR>
+
parameter/topology file is available it may be given with <B>-partop</B>.<BR>
  
As in <docmark>minAmber.pl</docmarl> the location of the Amber binary and
+
As in [[minAmber.pl]] the location of the Amber binary and
 
data directory are expected
 
data directory are expected
 
from the environment variables AMBERHOME, SANDEREXEC and LEAPEXEC. At least
 
from the environment variables AMBERHOME, SANDEREXEC and LEAPEXEC. At least
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attempt is made to locate the Amber binary from the search path and deduce the data
 
attempt is made to locate the Amber binary from the search path and deduce the data
 
directory from the binary location. The current version of this utility expects
 
directory from the binary location. The current version of this utility expects
Amber 7 or newer for full functionality.<BR><BR>
+
Amber 7 or newer for full functionality.<BR>
 
 
  
 
== Options ==
 
== Options ==
  
 
; -help : usage information
 
; -help : usage information
 
+
; -par key=value[,...] : Amber simulation parameters
 +
; -restart file : read restart file
 +
; -restout file : write restart file
 +
; -trajout file : write trajectory file
 +
; -final file : write final conformation in PDB format
 +
; -partop file : use given partop file
 +
; -log file : Amber log file
 +
; -elog file : Amber energy log file
 +
; -l [ca|cb|cab|heavy] force refpdb min&#58;max[=...] : restrain sampling outside specified residue range
 +
; -cons [ca|cb|cab|heavy] refpdb min&#58;max[_force][=...] : restrain sampling for specified residue range
 +
; -[no]translate : (do not) translate input PDB
  
 
== Examples ==
 
== Examples ==

Latest revision as of 03:55, 31 July 2009

Usage

usage:   mdAmber.pl [options] PDBfile
options: [-par Amberparams]
         [-restart file] [-restout file]
         [-trajout file] [-final file]
         [-partop file]
         [-log file] [-elog file]
         [-l [ca|cb|cab|heavy] force refpdb min:max[=...]]
         [-cons [ca|cb|cab|heavy] refpdb min:max[_force][=...]]
         [-[no]translate]

Show source


Description

This script is used to run molecular dynamics with Amber in a similar way as with mdCHARMM.pl which uses CHARMM instead. The options are very similar to minAmber.pl. At this point the focus is on running implicit solvent dynamics. Explicit water simulations are not supported yet but this feature will be added in the near future.

Output file names can be set with the following options: -final is used for the final conformation in PDB format, -trajout is used to request a coordinate trajectory file, and a restart file is written out with -restout. In a subsequent simulation, a restart file is read in at the beginning if given with -restart. No Amber parameter file needs to be generated prior to using this utility, but if an appropriate parameter/topology file is available it may be given with -partop.

As in minAmber.pl the location of the Amber binary and data directory are expected from the environment variables AMBERHOME, SANDEREXEC and LEAPEXEC. At least AMBERHOME should be set accordingly. Otherwise an attempt is made to locate the Amber binary from the search path and deduce the data directory from the binary location. The current version of this utility expects Amber 7 or newer for full functionality.

Options

-help 
usage information
-par key=value[,...] 
Amber simulation parameters
-restart file 
read restart file
-restout file 
write restart file
-trajout file 
write trajectory file
-final file 
write final conformation in PDB format
-partop file 
use given partop file
-log file 
Amber log file
-elog file 
Amber energy log file
-l [ca|cb|cab|heavy] force refpdb min:max[=...] 
restrain sampling outside specified residue range
-cons [ca|cb|cab|heavy] refpdb min:max[_force][=...] 
restrain sampling for specified residue range
-[no]translate 
(do not) translate input PDB

Examples