[gmx-users] problem while simulating metal ions
jestan1985 at yahoo.com
Wed Jul 7 03:36:24 CEST 2010
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. 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
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
Any suggestion is welcomed.
Thanks in advance.
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