[gmx-users] cyclic peptide dynamics. peptidic bond

[Giacomo Bastianelli]

I have been changing manually all the topology files 
(from the bonds, angles ecc...) but I constantly find
fatal errors during the minimization (example: atoms 
do not match, ecc..). I guess that it is really demanding
and difficult to change manually the topology file to have
gromacs recognizing a peptide bond that cyclize a protein.

any suggestion?

thanks

Giacomo


-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Tsjerk Wassenaar
Sent: martedì 24 ottobre 2006 10.08
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] cyclic peptide dynamics. peptidic bond


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 <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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