Respected Sir,
I have tried to minimize my pdb structure which is modeled by Modeller9v8. i use the Discovery Studio plateform to minimize this pdb structure by applying CHARMm force field and applying steepest descent and after that conjugate gradient algorithm. but the problem here is that the procheck result is not good as earlier. such as in Ramachandran plot 87% amino acids are in favorable region before minimization but after minimization only 55% amino acids are in favorable range...so plz sir suggest me some solutions....
Thanking you,
Your Sincerely
Probably you overdid it with minimization. Try a smoother energy minimization scheme, e.g. 500-1000 steps. Also bare in mind that molecular mechanics force fields are not designed to produce crystallographic quality structures. I would rather use Rosetta (or PyRosetta) or http://www.yasara.org/minimizationserver.htm if I wanted to improve atom clashes, dihedral angles, secondary structure, etc.
HTH, Thomas
On 30 April 2012 13:47, vishal Nemaysh vishal.bioinfotech@gmail.com wrote:
> Respected Sir, > > I have tried to minimize my pdb structure which is modeled by Modeller9v8. > i use the Discovery Studio plateform to minimize this pdb structure by > applying CHARMm force field and applying steepest descent and after that > conjugate gradient algorithm. > but the problem here is that the procheck result is not good as earlier. > such as in Ramachandran plot 87% amino acids are in favorable region before > minimization but after minimization only 55% amino acids are in favorable > range...so plz sir suggest me some solutions.... > > Thanking you, > > Your Sincerely > > -- > Vishal > Research Scholar, > University of Delhi, > North Campus > Delhi-110007 > M: 91+9650736653 > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >
Hi
87% of the amino acids in favorable region does not seems good to me. It means that 13% of the residues are in disallowed regions. It is a very significative percentage.
I think that the problem is with your model not with the minimization software.
Frequently I do minimization applying Charm force fields to protein-ligand models generated by Modeller and the results sometimes become better or at least the same.
Try to find better templates or generate a great number of models with Modeller and choose the best one.
Good look,
Flavio
--- On Mon, 4/30/12, vishal Nemaysh vishal.bioinfotech@gmail.com wrote:
From: vishal Nemaysh vishal.bioinfotech@gmail.com Subject: [modeller_usage] procheck problem. To: modeller_usage@salilab.org Date: Monday, April 30, 2012, 11:47 AM
Respected Sir, I have tried to minimize my pdb structure which is modeled by Modeller9v8. i use the Discovery Studio plateform to minimize this pdb structure by applying CHARMm force field and applying steepest descent and after that conjugate gradient algorithm. but the problem here is that the procheck result is not good as earlier. such as in Ramachandran plot 87% amino acids are in favorable region before minimization but after minimization only 55% amino acids are in favorable range...so plz sir suggest me some solutions....
Thanking you, Your Sincerely
-
flavio seixas -
Thomas Evangelidis -
vishal Nemaysh