AMBER Archive (2007)

Subject: Re: AMBER: van der waals parameters.

From: David A. Case (case_at_scripps.edu)
Date: Thu Mar 15 2007 - 13:30:34 CST

On Thu, Mar 15, 2007, Stefano Tonzani wrote:

> is it possible to define van der Waals parameters for PAIRS of atoms instead
> of having them defined for single atoms? For example, instead of
>
> CM 1.9080 0.0860
> something like
> CM CM 1.9080 0.0860
> CM CT 2.1000 0.0960
>
> or something similar? I tried this but of course it does not work.
> I am trying to implement some sort of coarse grained model and it is
> important that the nonbonded interactions are defined for atom pairs.

Doing this would require changes to the code the prepares prmtop files.
The vdW parameters are stored in a pairwise basis in the prmtop file, but
the parm.dat file (which is what LEaP uses to create prmtop files) only has
individual atom values, and uses a combining rule to get the pairs.

It's probably not that hard to modify LEaP do to what you want. If you don't
want to try to grok the LEaP source, you could just hand-edit the prmtop file
(or write a little script to do that).

...good luck...dac

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