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]
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.
- 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
- (do not) translate input PDB