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ffAMBER
Tools
AMBER force field ports for the GROMACS
molecular dynamics suite
Maintained by Eric J.
Sorin, Ph.D.
Assistant Professor, Department of Chemistry &
Biochemistry
California State University, Long
Beach
Tools listed here have been submitted by others and
are not maintained as a part of the ffAMBER ports. If you
have questions, concerns, bug reports, or other comments,
please correspond directly with the email address(es)
given below.
| amb2gmx.pl |
A perl script to convert AMBER topologies and
coordinates into GROMACS topologies and
coordinates. It requires an AMBER installation
(tested with AMBER 8 and AMBER 9). We have
frequently used it for converting small
molecule topologies and coordinates generated
using ANTECHAMBER to GROMACS format, although
in principle it should work for larger systems
as well. Please report any bugs that are found
to dmobley - at - gmail.com. No known bugs. To
give credit where credit is due, this is a tool
we updated and extended from one originally
written by E. Sorin in the Pande group. If you
use this script for a publication, you should
reference D. L. Mobley, J. D. Chodera, K. A.
Dill. "On the use of orientational restraints
and symmetry number corrections in alchemical
free energy calculations", Journal of Chemical
Physics 125:084902, 2006. [updated 28 May 2007]
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