On Mon, Aug 05, 2013, Changqing Yan wrote:
>
> (1) the results of nmode are the same as those produced
> by mmpbsa_py_nabnmode?
You should check this for yourself using a small example. That's the only way
to tell for *your* inputs.
>
> (3) As mentioned, the entropy I got is for the complex. if at the same time
> I want to get the according entropy for the protein and the ligand, what
> should i do? Extract the trajectory and then separate them into protein and
> ligand? If so, after I minimized them, the structure must deviate from
> those in the complex.
In this "single trajectory" approximation, the assumption is made that there
is no relaxation of the protein (receptor) when the ligand is unbound (and
ditto for the ligand). One generally doesn't know (without calculation)
how good or bad an approximation this is.
> In this situation, is the entropy data still reliable?
Depends on how you view the word "reliable". With it's usual meaning, none
of these entropy estimates are reliable.
...dac
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Received on Mon Aug 05 2013 - 09:00:03 PDT
