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 > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [EMAIL PROTECTED] Can't post? > Read http://www.gromacs.org/mailing_lists/users.php > -- 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
