Dear Jason, Thank you for your kind advise. I had fixed charge errors and I
am trying to use the MM/GBSA and MM/PBSA approaches as you suggested.
Best regards
2015-08-20 10:32 GMT-04:00 Jason Swails <jason.swails.gmail.com>:
> On Thu, 2015-08-20 at 10:09 -0400, Investigador Química wrote:
> > Dear Jason, thank you for your kind and clear explanation.
> > You are right. For the three isolated and solvated systems generated
> using
> > "solvateoct TIP3PBOX 11" we have:
> >
> > Box (x=y=z) triangulated 3-points waters sum of
> charges
> >
> > H-G 64,477 6598 -0.99950000
> > H 51,248 3254 -0.16460000
>
> This is concerning. Why is the charge of your system 0.16 electrons?
> You should try to find the underlying cause here and fix it.
>
> > G 37,612 1321 -0.03280000
>
> Same here.
>
> > My problem is how can I run the simulations with the water counts exactly
> > matched between the bound and unbound simulations?
> >
> > In AMBER tutorial 21 the following values are used for
> > water_tleap.in: solvatebox structure TIP3PBOX 16.50 iso
> > b2_tleap.in: solvatebox guest TIP3PBOX 13.16 iso
> > CB7_tleap.in: solvatebox host TIP3PBOX 10.18 iso
> > CB7_b2_tleap.in: solvatebox b2host TIP3PBOX 9.91 iso
> >
> > and manually they removed waters over 1500.
> >
> > In my case I do'nt know how to choose the appropriated number of waters
> or
> > the numbers of the
> > TIP3PBOX Nr? iso
> >
> > Could you please help me?
>
> This is not a common approach to computing interaction energies, and
> probably won't work. Usually people use an approach like MM/GBSA or
> MM/PBSA to do it. Interaction energies are usually computed from
> simulations of a *single* host-guest system, and postprocessing the
> trajectory. MM/GBSA and MM/PBSA analyses, as with LIE analyses I
> mentioned previously, make use of multiple trajectories, but the solvent
> is stripped out and treated implicitly.
>
> What you should do depends on what exactly you are trying to learn, or
> what precisely you are trying to compute.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
--
Área de Software
Investigación Facultad de Química
Universidad de Santiago de Chile
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Received on Sat Aug 22 2015 - 14:00:03 PDT
