MMTSB
Tool Set Documentation

mdAmber.pl

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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]
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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