[AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated.

From: giulia palermo <giulia.palermo83.gmail.com>
Date: Wed, 8 Jul 2015 10:14:39 +0200

Dear all,

we am parametrizing a Uracil base with an O3' terminus deprotonated.

As specified by the AMBER tutorial and done by Cornell et al. JACS 117,
1195, during the derivation of the Electrostatic Potential via QM
calculations, a methyl group is used for the capping of the O5', while the
O3' is capped with an hydrogen atom.
Subsequently, during the RESP fitting procedure, the TOTAL charge of the
capping metyl (.O5') and of the hydrogen (.O3') is set to ZERO.

In our case, this can not be done, because the O3' terminus should be
How do you suggest to proceed in such a way?

Thank you very much
Giulia and Lorenzo
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Received on Wed Jul 08 2015 - 01:30:04 PDT
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