No it is not in amber 10.
Which radii did you set in leap? This is very important.
On Mar 19, 2012 12:31 AM, "Aditya Padhi" <adi.uoh.gmail.com> wrote:
> Dear Dr. Simmerling,
> Thank you for the suggestions. Can you tell me is option igb=8
> is available in Amber 10? Also, can I know which radii you are talking
> about? If you can provide some additional detail on this, I will definitely
> mention which radii I am using.
>
> Thanking you,
> Regards
> Aditya.
>
> On Sat, Mar 17, 2012 at 4:50 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > 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.
> > > > > > > _______________________________________________
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> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Aron Broom M.Sc
> > > > > > PhD Student
> > > > > > Department of Chemistry
> > > > > > University of Waterloo
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> > > >
> > > >
> > > >
> > > > --
> > > > Aron Broom M.Sc
> > > > PhD Student
> > > > Department of Chemistry
> > > > University of Waterloo
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Received on Mon Mar 19 2012 - 04:00:03 PDT
