AMBER: hydrogen bonds

From: Jessica Koplin <>
Date: Fri, 1 Oct 2004 18:24:29 +0200 (MEST)


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
(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

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Received on Fri Oct 01 2004 - 17:53:00 PDT
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