Dear amber community,
If we have a covalent bond between the ligand and the protein, is it
still possible to use thermodynamic integration similar to what's
described in the tutorial ? Note that this is different from the case
where we have a mutating side-chain as described in the tutorial. Also
the charge of a covalently bound ligand will be different from a free
ligand. Do we need to add an extra step in the thermodynamic cycle or
just working with ligands with their complex-bound charge is enough?
I would also appreciate if you know any publications that discuss TI for
covalently bound ligands. So far I've only found a few papers that use
FEP but not TI.
Thanks,
Ali
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Received on Sun Aug 21 2022 - 23:30:04 PDT
