Re: [AMBER] parametrization of an RNA base

From: David A Case <>
Date: Sun, 6 Aug 2017 14:33:40 -0400

On Fri, Aug 04, 2017, giulia palermo wrote:
> I am parametrising an RNA base (i.e., guanine) which terminates with 5-OH
> at the end of the RNA chain.

It's hard to understand what you really want to do here. Nucleic acids
are by convention numbered from the 5' end to the 3' end, so having
"5-OH at the end of the RNA chain" doesn't make it easy to figure out what
you want.

I say this because you should check the existing "G3", "G5" and "GN" residues:
maybe they are close to what you want. Also, as the manual explains, there
is an "OHE" residue that may be helpful.


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Received on Sun Aug 06 2017 - 12:00:03 PDT
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