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.
Best,
--
Ilyas Yildirim
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- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Sun Oct 22 2006 - 06:07:33 PDT
