AMBER Archive (2006)

Subject: AMBER: HBON in frcmod file

From: Ilyas Yildirim (
Date: Sat Oct 21 2006 - 00:46:31 CDT

Dear All,

I have a system which falls apart when implicit solvent is used. The
system is composed of non-watson-crick bases; but it is experimentally
shown that has a stable structure (and most probably a helical structure).

When I created the necessary .frcmod parameters, I made some analogies
with similar structures. I defined the missing BOND/ANGL/DIHE/IMPR/NONB
parameters for these non-WC structures.

I will appreciate if someone can direct me what the HBON parameter is.
According the AMBER manual (pp. 85 of Amber 9 Manual), there is no
explicit H-Bond terms included in the amber force field. So what is the
use of this HBON term? And is it possible that because I did not define
this parameter in the .frcmod file, the structure is falling apart? I will
greatly appreciate any help on this. Thanks.


  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  -			-

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