On Fri, May 24, 2024, Abuhasan, Osama via AMBER wrote:
>
>For the free guest I got the same pKa value as the experimental one,
>but for pKa of the ligand in the complex I got a value far away for the
>experimental, In fact the pKa shift were surprisly correct but in the
>opposite direction.
You probably need to examine the contacts between the host and guest in the
complex, searching for reasons why the protonated form of the ligand is so
unstable in the complex. Force field limitations might be contributing to
the result, but there might be something in the structure that disfavors
protonation (equivalent to something that unfairly favors the deprtonated
state.)
...good luck...dac
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Received on Sat May 25 2024 - 15:00:03 PDT
