Sorry maybe I will make specific questions about the correct / recommended use of mmpbsa to compare a series of agonist with the same target protein:
1) is inp=1 the right choice?
2) Is there a standard reccomende set of parameters?
3) Is 1000 frames per point a good number?
4) How many repetitions (number of independent trajectories) should be run to have good sampling?
Thanks a lot,
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
> On 4 Dec 2021, at 12:39, Fabian Glaser <fabian.glaser.gmail.com> wrote:
>
> 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 - 05:30:01 PST
