[gmx-users] Re: amber force field in gromacs

Alan alanwilter at gmail.com
Sat Nov 21 12:22:50 CET 2009

Dear Leila,

Consider reading all about ACPYPI at acpypi.googlecode.com, specially the
wiki pages. Although you may not be interested in topology generation for
ligands, there's there important information about how to run amber force
fields in Gromacs environment.

And review carefully your ffamber installation. It looks I had some similar
issues in the past and although I never figured out what was the cause, a
simply careful reinstallation of ffamber solved the problem.

And if using amber force field, consider registering yourself at amber
mailing list (ambermd.org). I am suggesting that because as far as I know
from literature amber99sb is the most advanced force field from amber, yet
the year, but read:

Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., and
Simmerling, C. Compar- ison of multiple amber force fields and development
of improved protein backbone parameters. Proteins- Structure Function and
Bioinformatics 65, 3 (NOV 15 2006), 712–725.

However, I understand you want to do nucleic acids simulation rather than
proteins, so milage here is low and for that I suggested also the amber
mailing list.

I hope it may helps.


On Sat, Nov 21, 2009 at 11:00, <gmx-users-request at gromacs.org> wrote:

> Send gmx-users mailing list submissions to
> dear Mark
> your opinion is right [residue number 1 is NGLY in pdb file but residue
> number 1 is GLY in warning].
> howbeit, what work should I do?

Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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