[gmx-users] cyclic peptides

[Tsjerk Wassenaar]

Hi Giacomo,

Did pdb2gmx finish without errors? You have a cyclic peptide and
pdb2gmx will normally add N- and C-termini. You can override that by
using the -ter flag on the pdb2gmx command line and select "none" for
both termini. Then you have to edit the .top file and add the required
bonds, angles and dihedrals to make the peptide cyclic. Gromacs can't
do that for you (at present; maybe a -cyclic option in pdb2gmx for
peptides might come in handy if there is substantial demand for
simulations of cyclic peptides).

But I'm a bit concerned about the error genbox gives. It complains
that it can't find the topology you say you want it to read (-p
1KAL.top). If that is the topology you think you've generated with
pdb2gmx, check it's output and check your directory listing.

Best,

Tsjerk


On 10/20/06, Giacomo Bastianelli <gbastian at pasteur.fr> wrote:
> 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...
>
> thanks!
>
> giacomo
>
> 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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-- 
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