VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 15 2004 - 10:58:58 CDT

Jerry,
  I don't remember the previous question of this type that you
mention, but I'd recommend asking about that "maximum atom number
exceeded per group" error in one of the Charmm groups, since they
are much more likely to know what that means. Nobody in our lab
runs Charmm (they all run NAMD unsurprisingly) so none of the developers
here are likely to be able your question. Unless one of the VMD
or NAMD users on the mailing lists coincidentally know what Charmm's
atom number limitation is, you probably won't get any answers here.

Jim Phillips, the main psfgen/NAMD developer is out of town until late
next week, but he'd be the one with the most knowledge about your question.
Email namd_at_ks.uiuc.edu about this and he'll get to your question late
next week when he returns.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 15, 2004 at 08:28:15AM -0700, Jerry Xu wrote:
> Hey, All:
> I saw somebody asked the same question a while ago but never got
> response, since I met the same situation, so I just ask again here and
> really hope somebody know how to resolve the problem and like to share the
> tip---will really appreciate!!
> I use psfgen package in VMD to generate a PSF file for HIV-protease
> (1a30.pdb), I delete all non-protein atoms and only choose chain A. When I
> generate it as X-PLOR type (the default psf file type in psfgen), it has no
> problem to be used by NAMD , but when I generate it as charmm type, it
> can not be accepted by CHARMM----the error message is "maximum atom number
> exceeded per group". I tried with other smaller proteins then found out it
> seems psfgen just put all the atoms into one group. If the protein is small
> (under 50-60 residues), it is still okay for CHARMM, but when protein is
> little larger, CHARMM always complain too many atoms per group.
> Is here anyone know how to resolve the problem? I asked the guy who once
> post the similar question---he never get any answer from this mail list and
> just redo it with CHARMM....
>
> Thanks again
> Sincerely yours
> Jerry
>
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-- 
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                 Phone: 217-244-3349              
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