I don't think that "motion of ligand to protein" is desirable with
MMPBSA, which is calculated from an equilibrium trajectory.
Be sure to run through a tutorial:
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm
I recall that lack of treatment of Entropy can be an issue, also length
of the equilibrium trajectory.
Good luck. (It's been a few years since I tried this technique -
apologies in advance if I have been unhelpful).
On 4/9/2019 3:22 AM, MYRIAN TORRES RICO wrote:
> Hi all,
>
> I wanted to ask you a question about the mmpbsa program. I have
> performed my dynamics in my complexes and when I have done my
> calculations of mmpbsa on my files of final coordinates, I have
> obtained in the decomposition energy table, interactions in areas of
> the protein that in principle my ligand has not moved to them nor
> nothing ... I've visualized it and it's not even close ... How is it
> possible that I do this ...?
>
> Thanks in advance!
>
> Kinds regards,
>
>
> Myriam
>
>
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Received on Tue Apr 09 2019 - 20:00:02 PDT
