[gmx-users] Problem on forming bonds

[Kwee Hong]

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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