[gmx-users] problem while simulating metal ions

Mark Abraham mark.abraham at anu.edu.au
Wed Jul 7 09:05:29 CEST 2010

----- Original Message -----
From: Kwee Hong <jestan1985 at yahoo.com>
Date: Wednesday, July 7, 2010 11:36
Subject: [gmx-users] problem while simulating metal ions
To: gmx-users at gromacs.org

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> 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.

You probably need a custom residue in your .rtp that will match cadmium+residue. Consider how the heme residue works and develop something analogous.
> 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 manually? 

Yes, or get a working .rtp.

> 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.

That just asks for problems later. There's a good reason why simulating metalloproteins is a difficult topic - among other issues, you have to develop suitable parameters.

> 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. 

It's impossible for us to guess what's wrong here, a) because it's hard to understand what you mean by a water molecule being "attached with atom 279", and b) because we don't know what you've done to your .top file contents. Look at your starting, progress, and end configurations and see what makes sense.

Mark |

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