Re: AMBER: hydrogen bonds

From: Tim Meyer <>
Date: Tue, 05 Oct 2004 13:11:09 +0200

> can someone tell me if the criteria(distance, angles)
> for hydrogen bonds in RNA is the same as in proteins.
why should hydrogen bonds in protein and rna be treated differently?

there is no fixed h-bond definition:

ptraj 8 uses 3.5Ang and no angle cutoff as default
carnal used to have 4Ang and 120deg as default
other people used e.g. 2.5Ang (this is Proton-Pcceptor) and 135deg
(in this case Auffinger et al 1999)

hope it helps

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Received on Tue Oct 05 2004 - 12:53:01 PDT
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