Previously, something like happened to me, the solution that worked for me was to use acpype (code.google.com/p/acpype) and Amber FF. In this way, you could rule out problems related to the prodrg parameters.
Best regards, Aldo ======================================= Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx; aldoseg...@gmail.com ========================================= --- El jue 28-abr-11, Justin A. Lemkul <jalem...@vt.edu> escribió: De: Justin A. Lemkul <jalem...@vt.edu> Asunto: Re: [gmx-users] simulation with ligand at the active site A: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Fecha: jueves, 28 de abril de 2011, 1:02 onetwo wrote: > Hello Users, > > I have a query regarding simulation with the ligand. > > In my protein there are two ligands, one of them (coenzyme) is from the > crystal data, and other I have docked at the active site, while docking > it is showing good interaction with all the active site residues very > well. > I used GROMOS96 43a1 force field, and got the topology file made from > prodrg beta, using GROMOS 96.1 for both the ligands. PRODRG produces notoriously bad topologies. See, for instance: http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips > while doing equilibration I did, brendenson coupling on like > ; Berendsen temperature coupling is on in two groups > Tcoupl = V-rescale > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 300 300 > > and in MD simulation also > ; Berendsen temperature coupling is on in two groups > Tcoupl = V-rescale > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 300 300 > There could be some debate about these settings, and I do not know the best way to handle temperature coupling. It seems to me that if you have a ligand (or multiple) bound to a protein, the interactions between the protein and ligand(s) will be tightly coupled, such that you shouldn't lump the ligands into the "Non-Protein" group, which in this case likely comprises solvent. Maybe someone with more experience in these types of simulations can share some insight. > But after 1ns equibiration, one of the ligand (the one which I docked) > is going away from the active site and then I ran it for 4 ns further, > it has gone more far from the cavity. Following is the link to the snapshot > of the ligand at different time. > > https://picasaweb.google.com/118389174994698260649/Md_complex?authkey=Gv1sRgCMis2qry3cGj7AE#5600499037480314402 > > I want to ask if the change in the > position of ligand is justified with the parameters i have taken or it > if i have done something wrong? > Without providing the actual topology(ies) of the ligand(s) and a complete .mdp file, it is hard to say. But if you're using PRODRG output, I would suspect that it would be the culprit. -Justin > Thanks and Regards > > <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle?> > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
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