[gmx-users] problems with pdb2gmx command

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jan 22 19:34:06 CET 2009

Hi Jacob,

Check the output from pdb2gmx.
It works with the tutorial files, so the problem is with your input,
not with the program.


On Thu, Jan 22, 2009 at 5:39 PM,  <jaharvey at chem.umass.edu> wrote:
> I'm having issues with the pdb2gmx command in gromacs. It does not seem to be
> creating the .gro file for some reason. When I enter the command:
> pdb2gmx -f trial1.pdb -p trial1.top -o trial1.gro
> I only end with a trial1.top file but no trial1.gro file. However, the pdb2gmx
> command appears to work fine with the tutorial files that the developers have
> provided. Any suggestions? Thanks in advance.
> Jacob A. Harvey
> jaharvey at chem.umass.edu
> Chemistry
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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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