Hi
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
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Robert Fenwick wrote:
Hi,
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.
Bryn
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