[gmx-users] cyclic peptide dynamics. peptidic bond

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Oct 24 10:08:27 CEST 2006


You have to set the bonded terms correctly your self: bond, angles,
dihedrals, improper. Besides, you may have to list the 1-4
interactions under the [ pairs ] section. Check the manual on
topologies in case you're not sure what I'm talking about.
By the way, you could take an approach like this: if A is your
N-terminal residue and B is you're C-terminal residue, you need a B-A
peptide bond. Create the topology (using pdb2gmx) for such a dipeptide
and copy the terms for all inter-aa interactions to your cyclic
peptide topology, renumbering the atoms as required.



On 10/24/06, Giacomo Bastianelli <gbastian at pasteur.fr> wrote:
> I have a cyclic peptide and I would like to run a MD. unfortunately each
> time I run
> pdbgmx2, it changes the peptidic bond at the cyclization residues to a
> "messy" bond.
> I tried to fix it manually but it makes gromacs breaking the peptidic
> bond releasing
> the linear peptide during the dynamics.
> Thanks in advance!
> 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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