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
-------------------
Fabian Glaser
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
https://lokey.technion.ac.il/bioinformatic-knowledge-unit/
Tel +972 (0) 4 8293701
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Received on Sat Dec 04 2021 - 03:00:02 PST
