VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 09 2009 - 15:17:44 CST

Tom,
  My suggestion would be to try building the complete structure using
psfgen, presumably you could add the extra bonds from your special CONECT
records using a script. You could even do it in VMD itself for that matter,
using the "getbonds" and "setbonds" atom selection subcommands in some
combination with creative scripting.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Feb 07, 2009 at 07:02:30PM +0200, Thomas Evangelidis wrote:
> Dear VMD users,
>
> I have 3 separate .pdb files, the receptor, the co-crystalized
> inhibitor, and a potential inhibitor. I am trying to create one file
> (it doesn't matter if it will be .pdb or another readable format) that
> will contain all these 3 molecules in order to be able to measure
> Hbonds between them. However the bond information in ligand .pdb files
> (lines starting with "CONECT") pose a problem, as the atom indices
> between the 2 ligands clash. Moreover when I try to save the ligand
> coordinates as .pdb files no information about bonds is saved.
> The reason I'm asking all these is because I'm trying to render the
> receptor as NewCartoon and that drawing method work when loading the
> receptor .pdb but not when loading the complex with the 2 ligands.
>
> any advice would be deeply appreciated,
>
> Tom 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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