Re: Adding special VdW parameters

From: Axel Kohlmeyer (
Date: Sat Dec 25 2010 - 11:22:38 CST


On Sat, Dec 25, 2010 at 11:04 AM, Luca Bellucci <> wrote:
> Dear all,
> I need to simulate a system between Au surface and a protein.
> and I should define some special vdw interaction between a couple of kind atoms
> for example Au atom and S atom of the CYS residue. The standard sigma/epsilon
> of the S atom of the CHARMM/AMBER force field is not able to reproduce the
> "very strong interaction" (in this case might be a bond).
> Therefore I would like to strengthen this kind of interaction by adding a
> special vdw parameter only for the couple Au/S.
> Is there a feature/method to add extra vdw parameters for a couple of atoms?

in a charmm parameter file you have a section called NBFIX.
this is specifically meant to override non-bonded parameters
for specific pairs of atom types.

but don't get your hopes up too high as far as a realistic modeling
of the gold surface and its interactions with sulfur atoms goes.
this is rather complex and requires more sophisticated models
than what a typical bio-force field provides.


> For example the "extraBonds " feature presents in NAMD2.7 is conceptually very
> similar but it works only for internal coordinates.

> Thanks
>  Luca

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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