[gmx-users] amber force field in Gromacs

[servaas]

> servaas skrev:
> >> 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>
> >> Content-Type: text/plain; charset=UTF-8
> >>
> >> 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
> > never...
> >
> >> 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
> > here)
> >
> >> 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...
> >
> Well, it could. Are you using pbc or not? If you are then the rhombic
> dodecahedron will indeed cause the periodic copies to be more closely
> packed than for other boxes. I couldn't see any mentionong of pbc in
> your mdp file.
> 
> /Erik

Yes of course the box could make a difference, but what I meant was does
it make a difference if I create it in GROMACS or AMBER. I also tried
running without PBC and with larger boxes, without luck...


> >> 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
> > tleap -f leaprc.ff99SB
> > ad = sequence { DA5 DA DA3 }
> > saveamberparm da da_amber.top da_amber.crd
> >
> > ACPYPI or AMB2GMX
> > 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
> >
> >
> > GROMACS
> > 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)
> >>
> >>
> >>