I'll just add one comment. It sounds to me like you believe that the
appropriate chemical state of your uracil is with the O3' in a deprotonated
form. If this is true then you should NOT put a H on that oxygen during
the QM calculation. You only need capping groups for cases where an atom
will actually be bonded to another during your MD simulation -- that is,
the capping group allows that atom to have an environment in the QM calc as
similar as possible to what it will see during the MD simulation. If the O
will be deprotonated during MD, then it should also be deprotonated during
QM.
Hope that makes sense and that I've understood your situation properly.
Cheers,
Brent
On Thu, Jul 9, 2015 at 4:44 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
> Dear Giulia,
>
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#27
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract
>
> 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
> (Me-dimethylphosphate)]
> 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 http://q4md-forcefieldtools.org/REDServer-Development/
> 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
> ---
> http://q4md-forcefieldtools.org/FyD/
>
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>
--
_______________________________________________
Brent P. Krueger.....................phone: 616 395 7629
Professor................................fax: 616 395 7118
Hope College..........................Schaap Hall 2120
Department of Chemistry
Holland, MI 49423
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Received on Thu Jul 09 2015 - 04:00:02 PDT
