On Mon, May 21, 2018, daniele selli wrote:
>
> I am pretty new in the AMBER community and I am now facing an issue with
> the decomposition of the total energy.
Just a caution: Amber force field energies are not "pairwise
decomposable", and cannot be divided into to pieces representing parts
of the system. There are some ways to make approximations that get
around this, but even then, one has to make some rather arbitrary
assumptions (e.g. assigning the interaction terms between A and B to go
half to A and half to B.)
> PS: googling I have just found people calculating binding free energy
> with mmpbsa.py, but this is something different from what I want.
Assuming I haven't talked you out of doing this :=), tell MMPBSA.py that
you want to do a "stability" calculation: see section 31.3.4 in the 2018
Reference Manual.
...regards...dac
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Received on Tue May 22 2018 - 05:30:02 PDT
