[gmx-users] Problem on forming bonds

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jun 24 10:07:55 CEST 2010

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,


On Thu, Jun 24, 2010 at 9:05 AM, Kwee Hong <joyssstan0202 at gmail.com> 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
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

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