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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
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 <[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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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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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