Re: [AMBER] analyze residue charges after constant pH MD simulation

From: He, Amy via AMBER <amber.ambermd.org>
Date: Thu, 4 Jan 2024 18:50:49 +0000

Hi Zoey,

I assume you’re doing discrete (not the continuous) constant pH MD simulations. To get the total charge you could use the utility tool “cphstats”. The section in Amber 22 manual “26.7.2. Cumulative, running, and “chunk” averages” shows how to calculate a running average of fraction protonated per residue and their total. This total is a relative number to the lowest possible charge state of your system.

Hope this helps! 

--
Amy He
Hadad Lab . OSU
He.1768.osu.edu
From: Yang, Li-Yen via AMBER <amber.ambermd.org>
Date: Wednesday, January 3, 2024 at 1:05 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] analyze residue charges after constant pH MD simulation
Dear Amber Community,
I did a constant pH simulation on a protein complex system.
Since the charge of the titratable residues may change throughout the simulation, is there a way I can get the charges of all the protein residues in amber?
Also, does anyone know if there is any tool to visualize the charges of the residues?
Thank you!
Best,
Zoey
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Received on Thu Jan 04 2024 - 11:00:03 PST
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