help:autopsf changed the structure!

Date: Sun Nov 26 2006 - 19:57:42 CST

Dear all<p><p>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?<p><p>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.<p><p><p>Jin Tao<p>2006-11-27<p>

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