[AMBER] Mmpbsa inp=1 or inp=2

From: Fabian Glaser <fabian.glaser.gmail.com>
Date: Sat, 4 Dec 2021 12:39:40 +0200

Dear amberexperts,

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.

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.

Any expert suggestion what could be tried will be highly appreciated.

Have a nice weekend,

Fabian Glaser

Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel

Tel +972 (0) 4 8293701

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Received on Sat Dec 04 2021 - 03:00:02 PST
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