Re: [AMBER] Mmpbsa inp=1 or inp=2

From: David A Case <>
Date: Sun, 5 Dec 2021 09:04:44 -0500

On Sat, Dec 04, 2021, Fabian Glaser wrote:
>I am working on agonist ranking project, computing free energy for wt and
>mutants. I tried several MMPBSA input values, and it seems that inp=1 is
>better than inp=2. inp=1 values give values more similar to experimental
>values, at least for some examples.

My experience is limited and quite a bit out of date, but here goes: the
inp=2 option seems a bit more "fragile" than does the simpler inp=1 option,
especially for absolute binding energies. I too ran into cases where inp=2
gave very odd results, but the details are lost in the mists of time. Maybe
Ray and folks from his group can help here.

>I am running multiple trajectories, and I found the delta total values are
>very variable with a stdev of about +-3-5, specially for the mutants. I
>tried running very long simulations, but still the values drift a lot. I
>also tried different sampling using 500 or 1000 frames, but it did not
>improve the results.

Answers here are surely system-specific. Try using more frames, and/or
different length simulations. Note that you are looking for convergnence
here, not for agreement with experiment.

Be sure that your system is stable, and not always exploring new
configurations as time progresses. Check results for (say) the first half
of a given trajectory vs. the second half.

...good luck...dac

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Received on Sun Dec 05 2021 - 06:30:02 PST
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