Re: [AMBER] doubt in RMD

From: Jason Swails <>
Date: Thu, 27 Nov 2014 06:48:15 -0500

> On Nov 27, 2014, at 12:58 AM, Mary Varughese <> wrote:
> Sir,
> no such experimental data other than that they form canonical wc
> basepairs. i think about using it because sometimes the backbone
> seems to adjusts at the penality of breaking the hbonds ( especially
> terminals) .

It would be a mistake to think this is “unnatural” behavior. As I understand it, base pairs at the end “fray” quite frequently -- a phenomena that I believe has been observed and characterized experimentally. So I think this is a poor rationale to use these restraints, as they will artificially suppress the more “correct” behavior.

One other thing I’ll point out about base pairings in general -- the WC canonical base pairs do more to confer specificity than stability (i.e., mismatched bases are destabilized compared to “canonical” WC pairing, but the H-bonds in particular are not enough to “glue” the strands together). I think the Amber force field does a pretty good job of reproducing hydrogen bond strengths, so I would not suggest artificially increasing their strength through the use of restraints.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Nov 27 2014 - 04:00:04 PST
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