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

From: Jason Swails <>
Date: Wed, 8 Jul 2015 09:11:02 -0400

On Wed, Jul 8, 2015 at 4:14 AM, giulia palermo <>

> 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
> deprotonated.
> How do you suggest to proceed in such a way?

‚ÄčThe basic approach is to use capping groups to make sure you actually run
a QM calculation on a full molecule (not one with missing atoms and
dangling bonds -- that makes no sense in a QM calculation). However, you
never want the capping group to "steal" charge from the assigned partial
atomic charges of the fragment (since then you will wind up with a
non-integer charge). So when fitting charges, you apply the constraint
that the added fragments must carry a net neutral charge. This will make
sure that the fragment has the full charge you want.

It's not entirely clear why you say "this cannot be done because the O3'
terminus should be deprotonated". The net charge of all atoms you add to
your fragment should be constrained to zero. If you are simulating a
deprotonated 3' terminus, then your net charge on the QM region should be
-2, but the constraint on the added methyl group (and any other added atom)
should still be 0.

Or maybe I didn't understand your question/problem?


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jul 08 2015 - 06:30:02 PDT
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