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Difference between revisions of "mdAmber.pl"
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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. | + | 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>. | + | 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 | ||
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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. | + | 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]
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