> servaas skrev: > >> Message: 4 > >> Date: Tue, 1 Dec 2009 13:56:21 +0000 > >> From: Alan <alanwil...@gmail.com> > >> Subject: [gmx-users] Re: amber force field in Gromacs > >> To: gmx-users@gromacs.org > >> Message-ID: > >> <cf58c8d00912010556k5f2c918eqb2e1608c5c4cf...@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-requ...@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) > >> > >> > >> -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php