[gmx-users] Problem with genbox

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jul 16 09:25:15 CEST 2007

Hi Mark,

>From the log it seems you're trying to solvate your protein (-cp
gmx.pdb) with your protein (-cs gmx.gro)! Read the manual on genbox...


On 7/16/07, Mark Zottola <mzottola at gmail.com> wrote:
> I am trying to run genbox and am getting a segmentation fault.  After
> running pdg2gmx, I generated a gro file from the pdb outfput from pdb2gmx
> using editconf.  I then ran the editconf which seemed to run without
> problem.  Then I tried to use genbox.  It was at this point I received a
> segmentation fault.  I have attached the log file from genbox.
> As I am new user to Gromacs, I am trying to follow the spider toxin tutorial
> for my protein.  Any hints or pointers would be welcome.
> Thanks!
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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