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.
> > > > > > _______________________________________________
> > > > > > 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
> >
> _______________________________________________
> 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 Sun Mar 18 2012 - 22:00:03 PDT
