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 Fri Mar 18 2016 - 22:00:04 PDT
