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

From: FyD <>
Date: Thu, 09 Jul 2015 08:44:28 +0000

Dear Giulia,


In this approach 2 inter-molecular charge constraints are used between
hydroxyl groups of a nucleoside and methyl groups of dimethylphosphate.
that means
total charge (OH3'-nucleoside) + total charge (Me3'-dimethylphosphate) = 0
total charge (OH5'-nucleoside) + total charge (Me5'-dimethylphosphate) = 0

in your case, if I well understood your problem, you need to reach:
total charge (O(-1)-nucleoside) + total charge (Me3'-dimethylphosphate) = 0
   i.e. total charge (O(-1)-nucleoside) = -[total charge
total charge (OH5'-nucleoside) + total charge (Me5'-dimethylphosphate) = 0
ouf! to be tested...

You can obviously force the conditions, but the key question is, if
you break the fit or not because of the constraints (my guess is that
you will break the fit although you never know).
This can be easily checked by looking at the RRMS value (and r2 value)
from the RESP output.

if the fit is broken (RRMS increases a lot) (or r2 decrease) that
means you will have to find another strategy, another small molecule
instead of dimethylphosphate, or accept to live ;-) with bad charge
values for a part of your nucleoside fragment

Anyway PyRED at
should provide you a quick answer...

regards, Francois

> 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?

           F.-Y. Dupradeau

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Received on Thu Jul 09 2015 - 02:00:02 PDT
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