----- Original Message -----
From: Kwee Hong <jestan1...@yahoo.com>
Date: Wednesday, July 7, 2010 11:36
Subject: [gmx-users] problem while simulating metal ions
To: gmx-users@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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