VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 22 2006 - 17:45:34 CDT

Michel,
  Can you post the structure files on BioCoRE in the VMD Public project
so I can have a look at them? From the appearance of the message, you
either ran out of memory, found a bug in the PSF plugin, or something
else I didn't think of yet. We have a machine here with 32GB of memory,
so I should be able to load the 8 million atom structure with no worries.
You can get on the VMD biocore project by following the directions here:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

I'm heading out for some dinner, but if you upload the structure files
I'll try it out tonight.

  John

On Tue, Aug 22, 2006 at 05:36:39PM -0500, L. Michel Espinoza-Fonseca wrote:
> Hi John,
>
> It's me again. This time I got a problem where I'm unable to get any
> solution. I'm trying to add ions to a fairly big system (this time
> something around 8,000,000 atoms). I can solvate it with no problems,
> but when I try to run autoionize, I get the following:
>
> reading topology file
> /home/bscl2/espinoza/lib/vmd/plugins/noarch/tcl/autoionize1.2/ions.top
> >>>>>> SOD and CLA Ions Topology File <<<<<<<<<
> extracted from
> >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
> >>>>>>>>>>>>>>>>>>>>>August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> >>>>>>>Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
> >>>>>>410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
>
> Created by CHARMM version 27 1
>
> Autoionize) Reading monster-water.psf/monster-water.pdb...
> clearing structure, preserving topology and aliases
> reading structure from psf file monster-water.psf
> reading coordinates from pdb file monster-water.pdb
> psfplugin) Detected a Charmm31 PSF file
> Info) Using plugin psf for structure file monster-water.psf
> Segmentation fault
>
> And of course VMD crashes. I made stacksize and coredumpsized
> unlimited, but I got the same thing (VMD crashes). Do you have any
> suggestions on how to solve the problem? I'm using a workstation with
> 2 double-core Opteron and 4 GB of RAM.
>
> Thanks!
>
> Michel 

-- 
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
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078