Re: [AMBER] On QM/MM dummy atom and deprotonated TYR

From: Clorice Reinhardt <>
Date: Thu, 6 Feb 2020 18:27:38 -0500

Hi David,

I can't address the dummy atom question, but alternatively I just
parameterized the tyrosine residue in the deprotonated form following the
RESP procedure for the 20 canonical amino acids, created a lib file, and
ran MD from the get go with that. Which circumvents any issues with QM/MM
and other simulations. I'm not sure your actual end goal here, so i can't
say if this is the best plan of action for you-but that's how i proceeded.

Clorice Reinhardt

On Thu, Feb 6, 2020 at 5:39 PM David Sáez <> wrote:

> Hello everyone,
> I need a deprotonated TYR in my molecular dynamics simulation. I used
> parmed > changeProtState as suggested in many posts. It worked well for the
> MM part, but in the QM/MM section the software still "sees" the proton of
> TYR (I think it became a dummy atom during the MM simulations). Is there a
> way to keep it as a dummy atom?
> Thanks
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Received on Thu Feb 06 2020 - 15:30:01 PST
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