Hi,
Thank you for your response! Re-running the simulations wouldn't be possible for me since I'm short on time and the job scheduling system my school's server uses has a really long queue and i have to run 25 different ones for 100ns. My advisor said it'd be a good idea to find a way to just exclude those particular residues in the MMGBSA calculations, so I was hoping to compare the delta G values after excluding residues 40-51 to the delta G values I calculated before without excluding anything before deciding if it's worth the time to re-run the simulations.
Thank you!
On Aug 23, 2019 8:58 PM, David Case <david.case.rutgers.edu> wrote:
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 23 2019 - 20:30:02 PDT
