From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jul 26 2007 - 14:38:42 CDT

Unfortunately, people use the nomenclature you're referring to for two
different purposes: Either to indicate alternate conformations for a
single residue, or to keep the residue numbering consistent across a
family with the insertions indicated by the A, B, etc. The first of
those uses is more common, and thus it is what autopsf assumes: That
every definition of a given residue number after the first is an
alternate conformation. In your case, you're going to need to look at
the original literature on your protein, and find out why they used the
residue numbering they did. If you want to keep all of the residues,
just changing the residue numbering so that 22A is 22, 22B is 23, 23 is
24, etc. should be sufficient. Improving the handling of these rare
cases in autopsf is on my todo list, but has not happened yet.
Best,
Peter

snoze pa wrote:
> John,
> There is a pdb file 1JN0. If you try to run auto psf, do not use
> solvate etc. Then open both pdb files in vmd or pymol using
> 1JN0.pdb and the pdb file generated after the psf processing
> 1JN0_autopsf.pdb. you will find many gaps in psf PDB file.
> Check carefully the residue no 18,18A,18B in chain O of the same pdb file.
> Thanks for your attention and help
> s
>
>
> On 7/26/07, *John Stone* < johns_at_ks.uiuc.edu
> <mailto:johns_at_ks.uiuc.edu>> wrote:
>
>
> 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 <mailto: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
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu
> <mailto:johns_at_ks.uiuc.edu> Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/
> <http://www.ks.uiuc.edu/%7Ejohns/> Fax: 217-244-6078
>
>