[gmx-users] problem while simulating metal ions

Kwee Hong 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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