AMBER Archive (2006)

Subject: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!!

From: Christophe Guilbert (
Date: Thu Jun 29 2006 - 16:48:31 CDT

Dear Amber list (and Junmei ! ;-)))
When minimizing one of my ligand which include "ho" atom type, I found
that this atom collapsed (superimposed) with its nearest atom generating
a crazy electrostatic energy. this comes from the fact that "ho" (and
"hw") has a RDII and epsilon set to 0.0000 in gaff.dat:
  ho 0.0000 0.0000 OPLS Jorgensen,
  hw 0.0000 0.0000 OPLS Jorgensen,

Is it normal to find those parameter values in gaff.dat ???

Thanks for any thought.


Christophe Guilbert, Ph.D.
Mission Bay Genentech Hall
UCSF, Department of Pharmaceutical Chemistry
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