Re: Thiol on gold simulation in NAMD

From: Luca Muccioli (
Date: Thu Feb 26 2009 - 04:41:28 CST

dear Jorgen,

  in my opinion, if you know the geometry of the binding site you should use a
bonded Cu. if instead you want to predict it, you should use a non bonded

On the other hand a vdw site + one charge is a very poor description for
transition metals, and I agree with Axel's opinion, i.e. that you will
probably predict something "wrong", but maybe publishable.

To seek for a better parameterization you need qm calculations for
the parametrization and the effort is considerable.

An old idea that I never put at work was to use a multiple charge model for
copper (like for some water models), with 8 fractional charges of +0.25 in
octahedral or distorted octahedral positions, or maybe even nine charges or more
LJ sites etc etc.

if you like, try it ;)




Luca Muccioli, Ph. D.
Dipartimento di Chimica Fisica e Inorganica, INSTM
Universita` di Bologna
Via Risorgimento 4
40136 Bologna (Italia)

Phone: +39-051-6446992
Fax: +39-051-2093690

On Thu, 26 Feb 2009, Jorgen Simonsen wrote:

> Date: Thu, 26 Feb 2009 10:05:51 +0100
> From: Jorgen Simonsen <>
> To: Axel Kohlmeyer <>
> Cc:
> Subject: Re: namd-l: Thiol on gold simulation in NAMD
> Hi,
> 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
> Best
> J
> 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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