Giacomo,
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.
Best,
Tsjerk
On 10/24/06, Giacomo Bastianelli <[EMAIL PROTECTED]> 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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