Ni hao Kwee Hong, These special links should be defined in the file specbond.dat. That file you can find in the gromacs topology data directory. Have a look at the linkage of iron, e.g.. Also check the manual/wiki/mailinglist on 'specbond.dat' for more information.
Hope it helps, Tsjerk On Thu, Jun 24, 2010 at 9:05 AM, Kwee Hong <[email protected]> wrote: > Hi. > > I'm trying to subject a metalloprotein bound to cadmium to a molecular > dynamics. I've defined the cadmium ion in the atom type parameter file > (ffGa56a6.atp) and residue database (ffG53a6.rtp). And the bond length and > bond angle between the cadmium and sulphur of the metalloprotein had been > define in the force field file, too (ffG53a6abon.itp). As special bond is > expected to be formed between the sulphur of cysteine and the cadmium ions, > I've added the relevant information into specbond.dat. > > But when I run the pdb2gmx, there is no entries in the [ bonds ] and [ > angles ] for those bond length and bond angle. I've attached a sample of the > topology generated by pdb2gmx in the attachment. Please kindly refer to it. > And of course, as there is no entries in those parameter, there was no > cadmium-thiolate bond observed when I visualised the structure using pymol. > So, does that mean that I would need to add them on manually? > > To proceed with my simulation, I added the values in [ bonds ] and [ angles > ] manually. And as I do not have the relevant dihedral angle value from the > literature, I've deleted those entries in my topology file and continue to > prepare and subject the protein to energy minimization. During EM, the > potential energy of the system started to remain constant at step 124 and > eventually steepest descents converged to machine precision in 128 steps > with the maximum force is on atom 279 which would be one of the cadmium ions > in the system. When I visualised the system, one water molecule was found to > attached with atom 279, so I deleted that water molecule and subject the > system to em again. Yet the same thing occur after running for 49 steps. > What had gone wrong with my system? Is that cadmium molecule had been > running too far until it has gone out of the protein as water molecule are > not suppose to come into the protein. > > Any suggestion is welcomed. > > Thanks in advance. > > Regards, > Joyce > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
