Best Practices for Nucleobase Parameterization

From: Aaron Larsen (
Date: Mon May 18 2015 - 11:30:22 CDT

Hi all,

Sorry if this message is a repeat, it appears to have not been sent
earlier. I am attempting to parameterize some RNA like nucleosides using
the wonderful Force Field Tool Kit (VMD 1.9.2) and I have a few questions
to ensure that my results are relevant:

1) The keto tautomers are likely to be of lower energy but the geometry of
nucleobase amino groups should, strictly speaking, be tetrahedral in this
form. This, of course, is not what is normally depicted for nucleobase
amino groups which are commonly depicted in planar geometry, representing
some character of the enol tautomer. In this case, is it best practice to
force the geometry to be planar for the amino groups?

2) When modelling the water interactions, convention seems to be to only
consider interactions with the aminos, carbonyls, methyls, and hydrogens
that decorate the nucleobase but not the interactions involving the carbons
and nitrogens of the rings themselves. Is this best practice?

3) To simplify the calculations, I am working on just the bases and not
including the sugars. This seems to be the convention with these sorts of
projects. Is there any concern that ignoring the sugars in this way will
result in bad parameters (especially for charge) for the N1 atom?

Thank you for your consideration.


Aaron Larsen, Ph.D.
Harvard University Department of Chemistry and Chemical Biology
Harvard Medical School Department of Genetics
Mobile: 617-319-3782
FAX: 617-643-3328

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