Re: [gmx-users] Protein_model_refinement
On 6/10/2011 3:52 PM, shahid nayeem wrote: Dear All I want to refine a protein homology model, I did minimization but then procheck does not give better Ramachandran plot. EM can only do a local minimization, and there is no good reason why that should show a marked improvement on an arbitrary homology model. This model is a homodimer with each chain of 609 residue and a total of 1218 residue so a long MD simulation to search native state is not feasible. Can any one help me on this list to tell that how should I attempt this problem. Short MD will also be unlikely to do anything useful, because it is strongly determined by the initial conditions. So GROMACS is unlikely to be the tool you need for this problem, nor this list the place to find it. I would consult the homology modelling literature and software tools. Mark -- gmx-users mailing listgmx-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
[gmx-users] protein_model_refinement
Dear All I am trying to refine a protein model which is a homodimer with each chain having 609 residues.I tried minimizing in Chimera and then checking models with procheck.Infact model quality deteriorated as far as Ramachandran plot is concerned. Will doing MD simulation help me in Gromacs. It is a big protein so long MD simulation is not possible. Short duration MD will be insufficient to search native structure. I am stuck-up. Can anyone on this list help me. Shahid Nayeem -- gmx-users mailing listgmx-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
[gmx-users] Protein_model_refinement
Dear All I want to refine a protein homology model, I did minimization but then procheck does not give better Ramachandran plot. This model is a homodimer with each chain of 609 residue and a total of 1218 residue so a long MD simulation to search native state is not feasible. Can any one help me on this list to tell that how should I attempt this problem. Shahid Nayeem -- gmx-users mailing listgmx-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
