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 - 18:30:04 PDT
