AMBER Archive (2004)

Subject: AMBER: Question about dummy atoms

From: Sébastien Osborne (sosborne_at_science.uottawa.ca)
Date: Tue Jun 29 2004 - 12:16:30 CDT

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?

Thank you for your reponses

Sebastien Osborne
University of Ottawa

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