Re: Thiol on gold simulation in NAMD

From: Jorgen Simonsen (
Date: Thu Feb 26 2009 - 03:05:51 CST


Thanks for the answer although I hoped that it would be easy and not problem
to parametrize the Cu2+/Cu+ for a classical force field.

In my case I think the ion are pretty well integrated into the protein until
now I have used the parameters for Cu2+ from the article Deng et al
(doi:10.1529/biophysj.105.064444) where they have included it as 2+ and a
vdw parameter. The problem is that the coordination of one methionine
residues is not kept during the simulation which I would expect it to be -
in two of the other binding it is though so further investigation is needed.
My main question is would you include bonding parameters for the metal ion
and its interactions with its ligand like for example in the paper by Fuchs
et al.(doi:10.1002/jcc.20392) or Stote and Karplus where they as Deng use
the vdw along with its charge.

I know that many problems araises due to the d9 of Cu20 so I am really
puzzled how to proceed? Any suggestions or comments would be appreciated


On Wed, Feb 25, 2009 at 9:45 PM, Axel Kohlmeyer <
> wrote:

> On Wed, 25 Feb 2009, Jorgen Simonsen wrote:
> JS> A little question about the CPMD code and its possibilities:
> to get information about CPMD, please have a look at
> JS> The protein that I would like to simulate in the gold surface contains
> a
> JS> copper ion that I would like to play with the redox states of it 2+/+ -
> the
> JS> total system is 110.000 atoms with water or it is necessary to
> parametrize
> JS> the Cu2+/Cu+ for charmm?
> not sure whether it is possible to parameterize a classical force
> field with additive pairwise interactions only to represent a 2+
> cation well. people have done it and will do it, but the result
> will rarely be satisfactory, unless the cation is quite rigidly
> integrated into some framework.
> a.
> JS>
> JS> Thanks in advance
> JS>
> JS> J
> JS>
> JS>
> JS>
> --
> =======================================================================
> Axel Kohlmeyer
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.

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