[gmx-users] cyclic peptide dynamics. peptidic bond

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 24 16:42:56 CEST 2006

Giacomo Bastianelli wrote:
> 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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edit the specbond file to make a peptide bond. check the archives.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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