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 > >