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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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Charged ligands #8

Closed GHeinzelmann closed 3 years ago

GHeinzelmann commented 3 years ago

New approach needed to deal with charged ligands when DD is performed, due to artifacts caused by artificially setting the box potential at 0 for all lambda windows (gellium).

Chosen solution is to perform binding site (bound) and bulk (unbound) charging and discharging of the ligand simultaneously in the same box, keeping the overall charge of the box constant at zero.

GHeinzelmann commented 3 years ago

New branch for DD with charged ligands.