ffAMBER Tools
AMBER force field ports for the GROMACS molecular dynamics suite
Maintained by Eric J. Sorin, Ph.D.
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]
