[gmx-users] amber force field in Gromacs

Erik Marklund erikm at xray.bmc.uu.se
Tue Dec 1 23:46:55 CET 2009

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.

>> 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)

Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys

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