[gmx-users] cyclic peptides

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Oct 19 21:38:49 CEST 2006

Hi Giacomo,

You have to provide more information than that. Do you actually have a
file 1KAL.top (I expect not). How did you (or do you think you did)
create the topology? Using pdb2gmx? Please summarize what you did so
far and to get to the point where genbox fails on you?



On 10/19/06, Giacomo Bastianelli <gbastian at pasteur.fr> wrote:
> I have to run a md of a cyclic peptide.
> Does anybody know how to modify to have
> it running...
> actually I corrected the file and then run it.
> then I arrive at the step "genbox" and it write
> the top file but it says:
> file input/output error: 1KAL.top
> and then I keep having problems for the next steps...
> thanks
> giacomo
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Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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