AMBER Archive (2004)

Subject: AMBER: hydrogen bonds

From: Jessica Koplin (jessica_at_theochem.uni-frankfurt.de)
Date: Fri Oct 01 2004 - 11:24:29 CDT

Hi,

i am using AMBER to simulate an RNA-molecule
can someone tell me if the criteria(distance, angles)
 for hydrogen bonds in RNA is the same as in proteins.
I think in base paired
region one has other criteria than for example
in flexible loop regions.

What distance and angles cut-off do one use
for RNA or can one take the cut-off of proteins?
i have
N-H...0
0-H...0
(especially for the latter i am not very sure)
If someone has experience in this thing,
i would appreciate it very much, if you
can share this knowledge
with us.

thank you very much
in advance
for your help
jessica

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