VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 16 2004 - 17:45:08 CST

Hi,
  Take a look at the script I just posted to VMD-L for merging multi-frame
structures into a single PDB file. It implements much of what you need to
write out the N pdb files and merge them back together again. Take that
script and change the atom selection as needed and you ought to be able to
solve the problem you're working on as well. The script I wrote breaks up
the structure by chains since that worked for the particular
multi-structure PDB file I tested, but you could do it at whatever
granularity you need to make it work.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 16, 2004 at 04:18:49PM -0500, Satyavani Vemparala wrote:
>
> I have a DOPC coordinate file (PDB) in which the residue numbers is
> repeating. i.e.,
>
> side chains (OLEO) have residue numbers 1 & 3
> the head group (PCGL) has residue number 2
>
> and this repeats for all the lipid molecules (the last entry in every
> column has the the information about the lipid number e.g.,:
>
> ATOM 1 C1 OLEO 1 25.238 -18.360 17.677 0.00 0.00 L001
> ATOM 139 C1 OLEO 1 -10.888 -25.455 14.071 0.00 0.00 L002
>
> when iam trying to use psfgen to generate psf files, it does that only for
> the first lipid molcule and gives errors for all the other lipids:
>
> building segment U1
> reading residues from pdb file dopc-h.pdb
> duplicate residue key 1
> ERROR: failed on residue OLEO from pdb file
> duplicate residue key 2
> ERROR: failed on residue PCGL from pdb file
> duplicate residue key 3
>
> I guess the tedious way is to seperate each segment into a pdb file and
> then use psfgen (in which segment info is to be repeated 72 times!)
>
> But i was wondering if there is an easier way out of it.
>
> Thanks
> vani
>
>
>
>
>
>
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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