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

From: Christophe Guilbert <cguilbert.picasso.ucsf.edu>
Date: Thu, 29 Jun 2006 14:48:31 -0700

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 

-- 
--------------------------------------------------------------------------
Christophe Guilbert, Ph.D.
Mission Bay Genentech Hall
UCSF, Department of Pharmaceutical Chemistry
600 16th Street, Suite # S-126-D
San Francisco, CA  94143-2180 
for UPS/Fed Ex/DHL, change the zip code of 94107 for physical deliveries of package
Office      : 415-476-0707
Office fax  : 415-476-0688
Email: cguilbert.picasso.ucsf.edu
http://mondale.ucsf.edu
--------------------------------------------------------------------------
In a world without walls and fences,
who needs Windows and Gates?
        - Sun Microsystems
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jul 02 2006 - 06:07:13 PDT
Custom Search