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

From: giulia palermo <>
Date: Wed, 8 Jul 2015 16:20:56 +0200

Dear Jason,

thank you for your e-mail and sorry if I have not clearly explained my
Our Uracile has to be deprotonated at O3' in order to exert a specific

Thus, we are calculating the RESP charges for a deprotonated Uracile.
We have already parametrized nucleic acid bases using the capping
At that time, we have employed a methyl group for capping O5' and H for
capping O3'.
In this way, the TOTAL charge of the capping residues is ZERO.

In the case of a deprotonated Uracile, we can not cap O5' with a methyl
group. Indeed, the total charge of the methyl is 0.188 (NOT ZERO) and
during the refitting procedure, we would end up with a spurious charge,
because the TOTAL charge of the capping residues will not be zero.

How do you suggest to cap the O5' ??

Thank you
g & l.

2015-07-08 15:11 GMT+02:00 Jason Swails <>:

> On Wed, Jul 8, 2015 at 4:14 AM, giulia palermo <
> >
> wrote:
> > 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?
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Jul 08 2015 - 07:30:05 PDT
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