Dear Brent,
thank you for your email. We have parametrized the residue.
Of course, we let O3' as DEPROTONATED.
Thank you again
Giulia
2015-07-09 12:45 GMT+02:00 Brent Krueger <kruegerb.hope.edu>:
> 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/
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> _______________________________________________
> 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 - 09:00:08 PDT
