Thank you. I will check it out and get back to you.
On Wed, Mar 16, 2022 at 8:13 PM David A Case <david.case.rutgers.edu> wrote:
> 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 - 13:00:03 PDT
