Re: [AMBER] Question about running with a mask to exclude certain residues

From: A K <>
Date: Sat, 24 Aug 2019 03:03:32 +0000


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 <> wrote:

On Fri, Aug 23, 2019, A K wrote:

>Also, I received an error when trying to run to generate
>the new prmtop files to exclude residues 40 through 51 from my solvated

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?


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Received on Fri Aug 23 2019 - 20:30:02 PDT
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