Sir,
Infact i have tried multiple trajectory approach also (10 ns trajectory).
But didnt get any favorable result.
May be because i havent considered "make sure the average
delta G has converged by checking cumulative averages of all three
runs (complex, receptor, and ligand)". Would you please explain cumulative
average?
And also about entropy estimation. ? It would be really helpful.
Thanking you for your time and reply
mary
On Tue, Mar 22, 2016 at 6:09 AM, Ray Luo <rluo.uci.edu> wrote:
> Hi Mary,
>
> If you have a flexible ligand, the single trajectory approach is
> probably not the best way to go. Please try the multi-trajectory
> approach. Apparently, a key point here is to make sure the average
> delta G has converged by checking cumulative averages of all three
> runs (complex, receptor, and ligand). However, some sort of entropy
> estimation is also important to take into account the conformational
> flexibility in the delta G calculation.
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor
> Biochemistry, Molecular Biophysics, Chemical Physics,
> Chemical and Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Fri, Mar 18, 2016 at 9:48 PM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
> > sir,
> >
> > these are the files used to calculate PBTOT and entropy. I have done it
> > with other ligands(more rigid ligands) successfully. The problem here is
> > that the current ligand is half part flexible(a ch2-ch2-ch2-ch3 flexible
> > chain). Though the ligand bind experimentally and
> theoretically(throughout
> > the simulation time) the movement of the flexible region is causing
> changes
> > in PBTOT and entropy such that i cant get a statistically reliable value
> > (the final value obtained are highly positive; when i check the values
> (BE)
> > for each frame its deviating very much). The flexible part is causing
> that.
> >
> > So i would like to know which strategy i should be adopted in such cases.
> >
> >
> > thanking you for ur reply
> >
> > On Sat, Mar 19, 2016 at 6:43 AM, Ray Luo <rluo.uci.edu> wrote:
> >
> >> Mary,
> >>
> >> Maybe a bit more info is helpful, i.e. your inpu file. Also please note
> >> that mmpbsa single trajectory approach is more useful for delta delta G
> >> estimation.
> >>
> >> All the best,
> >> Ray
> >> On Mar 16, 2016 5:20 PM, "Mary Varughese" <maryvj1985.gmail.com> wrote:
> >>
> >> > Sir,
> >> >
> >> > I run some DNA-ligand1 complexes. Though the ligand remains bind
> >> throughout
> >> > the simulation, (the ligand binds experimentally also), I am not
> getting
> >> a
> >> > favorable binding energy from MMPBSA (single trajectory approach). The
> >> > ligand has a CH2-CH2-CH2 chain on one end which causes the ligand some
> >> > movement (entropy changes) and hence a stable binding energy is not
> >> > possible. Is there any other way to quantify the binding energy. Would
> >> you
> >> > please suggest a reliable approach in such situations where the ligand
> >> has
> >> > much flexibility?
> >> >
> >> > thanking you
> >> > mary
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Received on Mon Mar 21 2016 - 19:30:03 PDT
