Adding special VdW parameters

From: Luca Bellucci (
Date: Sat Dec 25 2010 - 10:04:55 CST

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


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