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?
Thank you for your time and kind advice in advance!
Thanks,
Amy
--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
he.1768.osu.edu
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Received on Mon Jul 19 2021 - 11:30:02 PDT
