Re: help:autopsf changed the structure!

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Nov 26 2006 - 22:13:22 CST

Could you please send pdb files from before and after the autopsf run?
Thanks,
Peter

taojinwuhan_at_sohu.com wrote:
> Dear all
>
> I modeled a protein by homology modeling, which Ramachandran Plot is
> good (90.9% residues are in the most favored region). Then I wanted to
> run a dynamics by NAMD, but when I examined the new pdb file generated
> by autopsf in vmd I found its Ramachandran Plot changed worse (only
> 38.8% residues are in the most favored region). I did not do anything
> else, what is wrong with it? Why the structure changed so much!? Can
> anybody give me some suggestions?
>
> Ps: the top file I used is top_all27_prot_lipid.inp, and my protein is
> a normal protein which has no metal ions and no other special atoms.
>
> Jin Tao
>
> 2006-11-27
>
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