VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 26 2007 - 11:29:58 CDT

Hi,
  What PDB code is the file that you're working with? Or is this
file generated from another package?

VMD itself doesn't care much about the residue numbering much as it
will create its own internal residue numbering. If you're trying to
build a structure for simulation however, you'll have to get
autopsf/psfgen/etc to be happy with the PDB however.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 25, 2007 at 02:29:51PM -0500, snoze pa wrote:
> Dear VMD user,
> I am using vmd to create autopsf file. I have multiple entry to same
> residues. If I will remove those residues then they are creating gap in the
> PDB
> structure. Can we use vmd to save multiple residues information. I have
> residues like 20,20A,20B.20C all four residues are different and have same
> residue number but if you want to delete them then it create a huge gap in
> PDB file. VMD is also not recognizing it and creating gap in the PDB
> structure. Any help?
> thanks in advance 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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