On Fri, Aug 23, 2019, A K wrote:
>Also, I received an error when trying to run ante-MMPBSA.py to generate
>the new prmtop files to exclude residues 40 through 51 from my solvated
>complex.
Note that it is far from clear that what you want to do (effectively
pretend that you originally ran the simulation without residues 40-51)
will give correct answers anyway (assuming you fix the syntax problems.)
Energies are not pairwise decomposable, and there is no "correct" way to
just remove part of the system: what remains can no longer be assumed to
be sampling from a Boltzmann distribution.
Is it really out of the question to re-run the simulation using the
parts of the protein that you want from the beginning?
....dac
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Received on Fri Aug 23 2019 - 19:00:01 PDT
