VMD-L Mailing List

From: Amarda Shehu (shehua_at_cs.rice.edu)
Date: Thu Mar 30 2006 - 16:50:02 CST

Hi,

I am trying to build a structure file with pfsgen for a circular protein.
I found out that the usual application of psfgen on a pdb file for a
circular protein does not recognize the fact that the first and last
residues in the protein are actually bonded. Terminal oxygens are added
instead automatically to the last residue. Does anyone know how to force
psfgen to put a peptide bond between the first and last residues?

Thank you,
Amarda.

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Amarda Shehu,
Graduate Student, Computer Science,
Rice University.
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