AMBER Archive (2004)

Subject: Re: AMBER: Question about dummy atoms

From: David A. Case (case_at_scripps.edu)
Date: Tue Jun 29 2004 - 12:24:56 CDT

On Tue, Jun 29, 2004, Sébastien Osborne wrote:

> Hi all, I have a little question about dummy atoms used in FEP runs.
> When a hydrogen atom disappears to become a dummy atom (type "DH"), what
> should the parameters of this dummy atom be? From my understanding,
> you give it zero vdw parameters and equilibrium values equal to regular
> hydrogen atoms (for bonds, angles, torsions) with the exception that I
> gave all those parameters very small force constants. I guess my
> question is should I use the small force constants or the regular force
> constants?

I recommend using "regular" force constants. These contributions will
cancel on two sides of a thermodynamic cycle.

...good luck...dac

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