VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Aug 22 2006 - 17:55:02 CDT

Sure! I'll do that later.

Thanks!
Michel

2006/8/22, John Stone <johns_at_ks.uiuc.edu>:
>
> 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
>