Re: [gmx-users] Protein_model_refinement

2011-10-06 Thread Mark Abraham
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

[gmx-users] protein_model_refinement

2011-10-05 Thread shahid nayeem
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

[gmx-users] Protein_model_refinement

2011-10-05 Thread shahid nayeem
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