Sir,
Thank you very much for the suggestions
I am using ambertols12. hope its ok.
Also MMGBSA is not suitable for nucleic acid systems. Isnt?
thanking you
mary
On Wed, Jul 24, 2013 at 7:29 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Mary,
>
> Most users use SCALE of 2. This is equivalent to spacing of 0.5
> Angstrom ... i.e. SCALE = 1/SPACING.
>
> By the way, if you are not using the latest AmberTools release, I
> strongly recommend downloading it for your project.
>
> Ray
>
> On Tue, Jul 23, 2013 at 10:49 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > On Tue, Jul 23, 2013 at 3:21 AM, Mary Varughese <maryvj1985.gmail.com
> >wrote:
> >
> >> Sir,
> >>
> >> I want to calculate binding energy of a nucleic acid ligand complex
> >> (explicit simulation , TIP3Pbox) using mm_pbsa.pl script.
> >> many values are explained for the input parameters
> >>
> >> It would be helpful if you can suggest the appropriate values
> >>
> >> * SCALE- lattice spacing in no of grids per angstrom. what value should
> i
> >> choose?
> >>
> >
> > Not sure on this one. If it was me doing the study, I would look at
> other
> > authors performing PB calculations on nucleic acids and look at their
> grid
> > spacing (especially useful would be a study that mentions why that value
> > was chosen or even better a systematic discussion of which values are
> > sufficient).
> >
> >
> >> * INP
> >> *SURFTEN and SURFOFF
> >>
> >
> > The default values of INP and SURFTEN/SURFOFF are probably best.
> >
> >
> >
> >> * IGB
> >> *GBSA
> >>
> >
> > I think this has been discussed on a previous thread (maybe even one of
> > yours, I can't remember). To reiterate the point, do _not_ use GB on a
> > nucleic acid system. It is known to perform badly and I would not trust
> > any results obtained from it.
> >
> >
> >> i dont understand which values should i choose and its significance.
> >>
> >> Also could i put MM= PB= GB= MS=1 to get binding energy without entropy
> and
> >> then again run the program with NM=1 to get the entropy calculation?
> >>
> >
> > Yes, you can do that.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
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> > AMBER.ambermd.org
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>
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Received on Tue Jul 23 2013 - 22:00:02 PDT
