From: John Stone (
Date: Wed Jul 16 2008 - 02:50:49 CDT

  This question is possibly better asked on the NAMD-L list since
there's generally more structure preparation activity going on in
that group of users and they'll likely know the topology/parameter
files etc...

  John Stone

On Tue, Jul 15, 2008 at 10:37:30AM -0700, wrote:
> This question is related to the VMD case study for light-harvesting in
> purple bacteria. I am attempting to setup a NAMD simulation for the
> acidophila-lh2.pdb structure included in the case study. To generate a
> .psf I created aliases for atoms and residues as needed like in the
> ubiquitin tutorial. However, I do not know how to treat certain residue
> names that are not present in the topology file, namely "BCL" for the
> bacteriochlorophylls, and "RG1" for the Carotenoids. Are there suitable
> aliases for these residues as well? I suppose this is as much of a
> bio-chem. question as a technical VMD one.
> I plan to edit the files from a perl script by calling psfgen in vmd text
> mode, btw.
> Thanks.

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