[gmx-users] cyclic peptide dynamics. peptidic bond

[David van der Spoel]

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.
________________________________________________________________________
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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