VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 15 2004 - 12:50:25 CDT

Hi,
  I'm forwarding Tyler's message since he's not subscribed to the list
and my list administration software is still not running yet so I can't
force-approve his post currently:

----- Forwarded message from owner-vmd-l_at_ks.uiuc.edu -----

Date: Thu, 15 Jul 2004 11:22:57 -0600 (MDT)
From: Tyler Luchko <tluchko_at_ualberta.ca>
To: Jerry Xu <jerryx_at_hotmail.com>, <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: vmd psfgen problem with CHARMM

Hi Jerry,

I assume that when you compiled CHARMM you probably used the default size
setting. Since CHARMM is written largely in Fortran there are builtin
size limits. To increase the limits try using LARGE or XXLARGE when you
compile. Be sure to delete build/platform/pref.dat first. You can see
the sizes of (almost?) all the variables this changes in
sources/fcm/dimens.fcm.

Hope this helps,

Tyler

On Thu, 15 Jul 2004, 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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>

Tyler

 ________________________________________________________________________
(_ Tyler Luchko Graduate Student _)
 _) Department of Physics University of Alberta (_
(_ Edmonton, Alberta, Canada _)
 _) 780-492-5519 tluchko_at_ualberta.ca (_
(________________________________________________________________________)

----- End forwarded message ----- 

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