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GHeinzelmann / BAT.py

The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems, compatible with the AMBER and OpenMM simulation packages.
MIT License
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running BAT.py on already execute simulations #38

Open amara86 opened 1 month ago

amara86 commented 1 month ago

Hi, I have already executed simulations for my membrane protein complexes, I have over 30 complexes. I have executed relative binding affinities and now want to execute absolute binding free energy calculations. Is there a way, I can use the same simulation data to execute BAT.py? Regards, Amara

GHeinzelmann commented 4 weeks ago

Hi, and thanks for your interest in the BAT code. In theory yes, but that would require some workaround to make it work. You could use your equilibrated complex and membrane without water as a starting point, treat the membrane molecules as cobinders, and then solvate everything again in the BAT workflow. But I have never tested something like this.

ErikZhang-9762 commented 4 weeks ago

Hi，Is it possible to control add solvents on the top and bottom sides of the membrane in the BAT workflow? Perhaps using parameterized parm7 and rst7 files as a starting point for input is an option?

GHeinzelmann commented 3 weeks ago

I think so, if you set the buffers on the x and y axes as 0 in the BAT input file, and the value you want for the z buffer, then it will solvate the system only on the z axis. But I am not sure about using parm7 and rst7 files directly, you could extract the membrane+protein+ligand coordinates from these files using cpptraj and then rebuild the systems with the new buffers.