AMBER Archive (2004)

Subject: Re: AMBER: hydrogen bonds

From: Tim Meyer (tim_at_mmb.pcb.ub.es)
Date: Tue Oct 05 2004 - 06:11:09 CDT

> 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

tim
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