Re: [modeller_usage] procheck problem.

[Thomas Evangelidis <>]

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 <" target="_blank">> 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  

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Vishal

Research Scholar,

University of Delhi, 

North Campus

Delhi-110007

M: 91+9650736653

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Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

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