[gmx-users] ATP, GTP and REX
mgoette at mpi-bpc.mpg.de
Thu Nov 29 15:09:33 CET 2007
You can use the AMBER ports for 3.3.2, I'd say.
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Robert Fenwick wrote:
> I would like to make some unrestrained simulations of ATP and GTP
> binding proteins and wondered if there were any topology files floating
> about for OPLSAA or the GROMOS96.1 forcefields for these two ligands?
> I understand that the gmx forcefields have been deprecated and that I
> should use one of the newer ones, however there are not that many ligand
> topology files about.
> I am just starting out, so any suggestions would be welcome. The systems
> are approximately 300 residues in size and I am interested in the
> stability and rms fluctuations of the systems.
> A secondary question is that of the AMBER forcefields, I am using the
> 3.3.2 version, however the amber files state specifically to use the
> port for the relevant version, one of which is missing for 3.3.2. Is it
> safe to use the 3.3.1 amber ff port with version 3.3.2 of GROMACS?
> Finally, if anyone can point me in the direction of a small test project
> that does some simple replica exchange, with some instructions as to how
> to get it to run, I would be very grateful.
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