AMBER Archive (2006)

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

From: Christophe Guilbert (cguilbert_at_picasso.ucsf.edu)
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,
JACS,110,(1988),1657
  hw 0.0000 0.0000 OPLS Jorgensen,
JACS,110,(1988),1657

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

Thanks for any thought.

Chris 

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