[AMBER] parametrization of an RNA base

From: giulia palermo <giulia.palermo83.gmail.com>
Date: Fri, 4 Aug 2017 14:48:01 -0700

Dear all,

I am parametrising an RNA base (i.e., guanine) which terminates with 5-OH
at the end of the RNA chain.

Following this tutorial:


one has to add ACE and NME as capping residues at the end of the
non-standard molecule.
My question is: having an RNA bases, which terminates with 5'-OH , how
shell I cap the 3' extremity?
Which residue shell I use as capping residue? And, in case the residue is
not ACE nor NME, which charges shell I assign during the RESP fitting

thank you very much

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Received on Fri Aug 04 2017 - 15:00:03 PDT
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