look in the manual at igb=8, it is our most recent GB parameter set and we
believe it is much better than the other options for proteins.
Note that the radii you choose in Leap also has a large impact on the
results. you don't say which radii you chose.
On Sat, Mar 17, 2012 at 2:19 AM, Aditya Padhi <adi.uoh.gmail.com> wrote:
> Hi Aron,
> Yes, I will try with alpb=1; it may be helpful. Well. I will let you
> know once I will do the MD runs.
>
> Thanks a lot for your suggestions.
> Regards
> Aditya.
>
> On Sat, Mar 17, 2012 at 11:36 AM, Aron Broom <broomsday.gmail.com> wrote:
>
> > 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.
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > 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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> > > 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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Received on Sat Mar 17 2012 - 04:30:03 PDT
