[gmx-users] Can not open file: topol.tpr

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 5 15:20:40 CET 2009


You mentioned it was from following a tutorial. In that case also
always check whether your line reads exactly the same as is stated in
the tutorial. Besides, indicate which tutorial, as there are many, and
if you find that it was an error in the tutorial rather than your
typo, also report that to the author of the tutorial (which, in any
case, is likely to be subscribed to the user list).



On Tue, Mar 3, 2009 at 9:32 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> drugdesign wrote:
>> Oh, I am very sorry, I've copied the wrong error.
> That's life - but one needs to be methodical and exacting with science in
> general and computational chemistry in particular.
>> Actually error was with the same tutorial at the next step with mdrun -v
>> deffnm em.
>> I can't figure  out why I need topol.tpr for energy minimization? It must
>> be only em.tpr, right? by -v deffnm command?
>> -------------------------------------------------------
>> Program mdrun, VERSION 4.0.2
>> Source code file: gmxfio.c, line: 736
>> Can not open file:
>> topol.tpr
>> -------------------------------------------------------
> Well, at least you copied and pasted your mdrun command line correctly, but
> you didn't form it correctly in the first place. It needs to be
> mdrun -v -deffnm em
> There are default file names for all files supplied by options to GROMACS
> programs. If GROMACS can't interpret the information you supply, you might
> get such an error when it also can't find the default necessary filenames.
> 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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