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
> > >
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 16 2012 - 23:30:04 PDT
