dmobley at gmail.com
Thu Mar 16 01:04:55 CET 2006
GAFF is the Generalized Amber Force Field, and contains AMBER force
field parameters for a lot of small molecules. The AMBER force field
itself has been ported to GROMACS by the Pande group, but the last
time I checked they had no plans to port GAFF.
However, I do currently use GAFF with GROMACS by setting up small
molecules using the antechamber package (which is distributed with
AMBER, or can be downloaded directly from the Antechamber web page).
Then, we have a conversion script we've written together with the
Pande group which can turn AMBER topology and coordinate files in to
GROMACS topology and coordinate files. So my approach is to run small
molecules through ANTECHAMBER to get GAFF parameters and then convert
their topologies to GROMACS.
We'll probably be making the conversion script available on the web
(at the AMBER port website) in the near future (at which point I'd
send an e-mail to this list) but in the meantime you can get a copy by
e-mailing me directly. It is a "use-at-your-own-risk" script, in that
we don't guarantee it works properly. However, it works fine for us.
Incidentally, if you use antechamber, you need at least version 1.2.4,
if I remember correctly. Previous versions (such as that distributed
with AMBER 8) omit some improper torsions.
Hope this helps.
On 3/14/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 日産化学 石川誠 wrote:
> > Hi all,
> > I'm searching forecefield for a small molecule.
> > Dose anyone know how to get GAFF for GROMACS?
> more info please
> > Thank you for your time.
> > MAKOTO ISHIKAWA
> > _______________________________________________
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> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
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