AMBER Archive (2006)

Subject: AMBER: How to set Bondi Radii using xleap

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Aug 01 2006 - 00:40:15 CDT

Dear All,

Is there any way to set the bondii radii to zero or any value for a
specific atom type using xleap? I do it manually, and I was wondering if I
can do it using xleap somehow.

Another question is the following: When the bondii radii for a specific
type is set to zero, and igb=2 is used, I am getting NaN results in the
output file (when bondii radii is not zero - even when it is very close
to zero - the result is ok). I was wondering why this is creating a
singularity in the system when implicit solvent is used. Thanks in
advance.

Best, 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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