On Wed, Mar 16, 2022, Soumyajit Karmakar wrote:
> I am doing a QM/MM MD simulation with DFT
>level of theory. My ligand is a zwitter ionic ligand present in a protein.
>Now during the simulation the ligand in active site is not retaining it's
>zwitter ionic state but becomes some neutral one like NH2 and COOH.
Did a proton move from the NH3 over to COO- during the simulation? That
suggests that the environmental (electrostatic) stabilization of the
zwitterion form is not strong enough to prevent the isomerization. Look at
an animation of the trajectory, and study the close surroundings to see
what should be stabilizing the zwitterion form.
(Make sure that the ligand is not in the neutral form at the start of the
simulation -- if that is the case, you have some problem in system setup.)
...good luck....dac
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Received on Wed Mar 16 2022 - 08:00:03 PDT
