[gmx-users] amber force field in Gromacs

servaas servaas.michielssens at student.kuleuven.be
Tue Dec 1 16:31:43 CET 2009

> Message: 4
> Date: Tue, 1 Dec 2009 13:56:21 +0000
> From: Alan <alanwilter at gmail.com>
> Subject: [gmx-users] Re: amber force field in Gromacs
> To: gmx-users at gromacs.org
> Message-ID:
>         <cf58c8d00912010556k5f2c918eqb2e1608c5c4cfaa9 at mail.gmail.com>
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> 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 generated own parameters, had an error tried to find out the problem,
eventually I  tried with natural NA and got exactly the same problem.
(The modified molecule was very similar to natural nucleic acids)
> 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.
True, but as all ready stated, in AMBER I can simulate this compound without any problems in vacuum. 
I also ran the simulation in gromacs with a solvent box and counter ions, same problem. 
So it is not a vacuum artefact.

> 2) Have you try to use pdb2gmx to generate your files from your pdb
> directly to GMX?
Not yet, I could ideed try this for the natural sequence, but the
problem persists then for my modified molecule...
> 3) When you say that gmx double precision works, is your system in
> vacuum or with solvent?
Double precisions works both in solvent and in vacuum, single precision
> 4) if using tleap, create your system with solvent and ions and then
> use acpypi to convert to gmx.
What problems do you expect from creating it in amber without solvent
box and creating the box in gromacs? I applied this procedure before
with success. (although this was with amb2gmx.pl, which I also tried
> 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?).
Do you realy expect serious problems from this? Creating a molecule in
vacuum and adding the box in GROMACS looks perfectly ok to me. Adding a
box only adds a line in the .gro file about the box parameters, I do not
see how this could influence anything else...
> I would ask you to give more details and even a detailed step by step
> of commands of what you're doing including tleap.

Ok, to keep things simple for the case of the natural NA:
tleap -f leaprc.ff99SB
ad = sequence { DA5 DA DA3 }
saveamberparm da da_amber.top da_amber.crd

python acpypi.py -x ad_amber.crd -p ad_amber.top -o gmx -b ad_gro
or with amb2gmx.pl
./amb2gmx.pl --prmtop ad_amber.top --crd ad_amber.crd --outname ad_gro

editconf -bt dodecahedron -d 1.0 -f ad_amber.gro -o ad_box.gro
I run a minimization:
grompp -f md.mdp -c ad_box.gro -p ad_gro.top -o em.tpr
mdrun -deffnm em
(Also tried putting a position restraint step in between, did not
resolve the problem)
grompp -f md.mdp -c em.gro -p ad_gro.top -o md.tpr
mdrun -deffnm md
> Regards,
> Alan
> 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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