[gmx-users] cyclic peptides

Giacomo Bastianelli gbastian at pasteur.fr
Fri Oct 20 09:13:43 CEST 2006

I have the top file and I create the topology file using pdb2gmx.
I then generate with editconf the water box.

after that genbox fails...



Tsjerk Wassenaar wrote:
> 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
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