MMTSB
Tool Set Documentation

Difference between revisions of "mdAmber.pl"

From MMTSB
Jump to: navigation, search
Line 11: Line 11:
 
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>
Line 19: Line 19:
 
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 [[minAmber.pl]] the location of the Amber binary and
 
As in [[minAmber.pl]] the location of the Amber binary and
Line 27: Line 27:
 
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 ==

Revision as of 03:50, 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


Examples