Well, I guess if you are going to be exhaustive, you should test all the
relevant igb settings (1,3,5,7 I think?), and also the linearized poisson
boltzman one, I think you specify alpb=1 or something of that sort, it's
right after the igb stuff in the amber 11 manual.
best of luck.
On Sat, Mar 17, 2012 at 1:57 AM, Aditya Padhi <adi.uoh.gmail.com> wrote:
> Hi Aron,
> I have tried with igb=5, but not achieved any desirable conformations
> of my protein of interest as compared to Explicit solvent MD runs. I will
> try with igb=7 and different parameters. If you have any other suggestions,
> then do let me know.
>
> Thanking you,
> Regards
> Aditya.
>
> On Sat, Mar 17, 2012 at 11:23 AM, Aron Broom <broomsday.gmail.com> wrote:
>
> > Well, you could try different implicit solvation models. The manual goes
> > into some detail about these, igb=5,7 and such. I'm not an expert, but
> I'm
> > not sure that you are necessarily going to see better agreement, it's a
> > huge change to go from explicit to implicit solvation.
> >
> > On Sat, Mar 17, 2012 at 12:29 AM, Aditya Padhi <adi.uoh.gmail.com>
> wrote:
> >
> > > Dear Amber users,
> > > I want to run Implicit solvent MDs with my protein of interest.
> I
> > > have already simulated the protein using explicit water model TIP3P. I
> > want
> > > to yield the results in better agreement/ similar conformations like
> that
> > > of explicit solvent runs. But I am not getting the same results. Can
> any
> > > one please suggest what are the best parameters to achieve results
> using
> > > implicit solvent that can mimic the results of explicit solvent MD
> runs?
> > >
> > > Thanking you,
> > > Regards
> > > Aditya.
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Aron Broom M.Sc
> > PhD Student
> > Department of Chemistry
> > University of Waterloo
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Fri Mar 16 2012 - 23:30:03 PDT
