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

Alan alanwilter at gmail.com
Tue Dec 1 14:56:21 CET 2009

Dear Servaas,

I've been following your thread. I am the developer of acpypi and
thanks for giving a try.

So, as you may already know, you are trying acpypi as amb2gmx.pl so
far, but you also seemed to have read acpypi wikis and realise that
acpypi can help you to generate the whole topology for a ligand.

However, AFAIU you have only regular NA and not modified ones neither
ligands, right? But then why are you using RED?

I understand your approach about using tleap to create your whole
system and then convert it to GMX. It should work at first but it is
clearly not as you reported.

So, here goes some of my recommendations:

1) GMX is vacuum is unrealistic and prone for errors. There's no GB
implementation as far as I know.

2) Have you try to use pdb2gmx to generate your files from your pdb
directly to GMX?

3) When you say that gmx double precision works, is your system in
vacuum or with solvent?

4) if using tleap, create your system with solvent and ions and then
use acpypi to convert to gmx.

The use of amb2gmx or acpypi is to give you a system to be run
immediately in gromacs doing just a grompp and mdrun. Using editconf
will change the parameters of your box and it may have serious
implications besides that in amber we don't have dodecahedron, so if
doing what you're doing then you're not replicating the conditions you
have in amber with those in gmx (although it puzzles me that gmx
double works, with the commands you gave in gmx?).

I would ask you to give more details and even a detailed step by step
of commands of what you're doing including tleap.


On Tue, Dec 1, 2009 at 11:00,  <gmx-users-request at gromacs.org> wrote:
> Thanks for your suggestion, I tried  without success and  I also tried
> shake. But this is also rather fighting the symptoms than the cause...
> And amber simulations in vacuum do work fine... My personal guess was
> that another parameter in my mdp file was not compatible with the amber
> force field, but I could not figure out which one. I also tried
> different settings, e.g. the one I found on the acpypi wiki.

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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