VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 20 2007 - 13:31:15 CDT

Other than a few key atom names (e.g. "CA", various hydrogens, etc) VMD
doesn't worry too much about the atom types for the purposes of display.
If the PDB file contains the chemical element symbol in the ATOM records,
then VMD will recognize all of the atoms more accurately, even in the case
that unusual atom names are assigned. VMD tries to be somewhat permissive
in accepting whatever you throw at it where possible. Plugins like
autopsf and paratool need much more specificity however and they employ
their own rules for atom typing etc.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jul 20, 2007 at 10:52:48AM -0700, Arneh Babakhani wrote:
> Hi
>
> I'm trying to manually adjust some pdb files obtained from another
> software package (Accelyrs's Discovery, which outputs the pdb of a
> structure with some odd atomtypes).
>
> I was wondering, does there exist a list of atom types that VMD readily
> recognizes, when reading in a PDB? (I browsed through the manual and
> mailing lists, didn't see anything).
>
> Thanks,
>
> Arneh
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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