Re: [AMBER] The protonation state model of TYR in CpHMD

From: Adrian Roitberg <>
Date: Mon, 19 Jul 2021 17:26:44 -0400

On 7/19/21 2:14 PM, He, Amy wrote:
> [External Email]
> Dear Amber Community,
> I have been doing constant pH MD simulations with Amber, and I have some questions about the protonation state model of the tyrosine residue.
> I noticed that the tyrosine residue has only two states: protonated and deprotonated. So I wonder how the position of the hydrogen atom HH (the phenyl group hydrogen) is determined, when the anionic tyrosine becomes protonated. According to the description of the protonation state models, a deprotonated residue would have a “ghost” proton at the ionizable position.
> For the tyrosine residues, is this “ghost” proton still counted in the bonded (bond, angle and torsional) potential and VDW interaction? If the SHAKE algorithm is used for the other hydrogens in the simulation, is the “ghost” proton also constrained by SHAKE?


Is all of these cases, when we switch from protonated to unprotonated,
what happenes is that the proton one 'removes' is still there, as you
said, but its charge is zero and so is it vdw parameters.

Bond, angles, torsion s are all still being computed, but by turning off
electrostatics and vdw, those energies are not counted when trying to
change protonation state or when doing dynamics in the unprotonated state.

The proton, even as a ghost, still moves around and it can change
rotation. Once you protonate it again, it just stays where it is from
when it was a ghost, but now it acquires charge and vdw energies.

Is this ok ?


> Thank you for your time and kind advice in advance!
> Thanks,
> Amy
> --
> Amy He
> Chemistry Graduate Teaching Assistant
> Hadad Research Group
> Ohio State University
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Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
AMBER mailing list
Received on Mon Jul 19 2021 - 14:30:02 PDT
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