Hi Amy,
Thank you SO much for answering so many questions I posted 😊
I am wondering how you found out about this information.
(Did you find it from the manual? I am just curious because I don’t recall seeing it from the tutorials/manuals etc.)
Zoey
From: He, Amy <he.1768.buckeyemail.osu.edu>
Date: Tuesday, February 6, 2024 at 7:10 PM
To: Yang, Li-Yen <zoeyxyang.gatech.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] constant pH protonation states
Hi Zoey,
Is this somehow supposed to be like this for AS4 and GL4 in constant pH?
Yes. Titratable ASP/GLU in constant pH MD simulations have four distinct tautomeric states when they are protonated. Each oxygen can be protonated on the anti- or syn- position.
Does the pdb file (converted from the trajectory files) from the constant pH reflect the actual protonation state?
The structures however do not incorporate the actual protonation states. Often you just get the equilibrium ratio by counting the occurrences of the protonated/deprotonated forms from a collection of sampled structures with variable protonation states. If you want to know the protonation state of a residue at a specific time point, you can look into the .cpout file. It might be possible, with some scripting, to export a trajectory with the protonation states incorporated. But it seems like most people perceive the trajectory as a collection of sampled states not a time evolution.
Hope this helps!
--
Amy He
Hadad Lab . OSU
He.1768.osu.edu
From: Yang, Li-Yen via AMBER <amber.ambermd.org>
Date: Tuesday, February 6, 2024 at 6:43 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] constant pH protonation states
Hello,
I have finished a constant pH simulation in explicit solvent.
One thing I noticed that is confusing to me:
When I visualize the protein side chains, I found that the carboxylic acids on Asparate and Glutamate, have two hydrogens attaching to each of the oxygen. (as shown in the picture below: )
[cid:image001.png.01DA592B.5F7A0930]
I am confused about why this is happening. The hydrogens were added by tleap before I run the simulations.
I saw some comments here (
https://urldefense.com/v3/__http://archive.ambermd.org/201508/0476.html__;!!KGKeukY!3ErMXeoeK3NUf75fi_-dPwPHNdotFpPEQhtiKOpzD-0B0lININw7az8e_tEUA_wg6aj6EnSz8cnh2bV3L4CJBfp84ZI$
) about 4-hydrogen carboxylate groups. But I don’t understand why there are two hydrogens on a single oxygen.
Is this somehow supposed to be like this for AS4 and GL4 in constant pH?
Does the pdb file (converted from the trajectory files) from the constant pH reflect the actual protonation state?
Thank you very much!
Zoey
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Received on Tue Feb 06 2024 - 17:00:02 PST
