VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Apr 02 2006 - 20:14:28 CDT

Hi,
  Regarding the psfgen side of things, you'll have to talk to the
psfgen author, Jim Phillips (jim_at_ks.uiuc.edu) about psfgen-specific
questions as the psfgen code is independent of VMD.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 30, 2006 at 04:50:02PM -0600, Amarda Shehu wrote:
>
> 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.
>
> ***********************************
> Amarda Shehu,
> Graduate Student, Computer Science,
> Rice University.
> *********************************** 

-- 
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