[gmx-users] cyclic peptides

[Tsjerk Wassenaar]

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?

Best,

Tsjerk

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
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>


-- 
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