Hi Zoey,
The utility script, cpinutil.py, has the “describe” option to print the definitions of defined protonation forms.
The usage is documented in Amber 22 Manual, 26.2, pp. 562.
If I remember correctly to inquire about GL4 you do:
cpinutil.py –describe GL4
From: Yang, Li-Yen <zoeyxyang.gatech.edu>
Date: Wednesday, February 7, 2024 at 6:33 PM
To: He, Amy <he.1768.buckeyemail.osu.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] constant pH protonation states
Hi Amy, Thanks for sharing the helpful information! It’s super helpful! By the way, do you know where we can find information of what each state of titratable residues represents exactly in constant pH simulation? (I am hoping to understand
Hi Amy,
Thanks for sharing the helpful information! It’s super helpful!
By the way, do you know where we can find information of what each state of titratable residues represents exactly in constant pH simulation?
(I am hoping to understand what the protonation states are like for each titratable residue. For example, what do state 0~state4 look like for AS4?)
I wasn’t able to find any information from the manual or tutorials. I’m wondering how you found out about it.
Thanks so much again!
Zoey
From: He, Amy <he.1768.buckeyemail.osu.edu>
Date: Tuesday, February 6, 2024 at 8:13 PM
To: Yang, Li-Yen <zoeyxyang.gatech.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] constant pH protonation states
Hi Zoey,
Thank you for your kind words. Happy to know if anything I said helped 😊
The official manual has been a great resource for me. The publications on the methodology and applications might be useful too, if you are interested in how the constant pH MD protocol was implemented and improved with times in Amber. I also want to mention that when I began to learn this method in Amber, Dr. Jason Swails website was very helpful: http://jswails.wikidot.com/<https://urldefense.com/v3/__http:/jswails.wikidot.com/__;!!KGKeukY!wZNX2YiN_eq6JSrKlnmbz-TETAoCCMw_idyS103SRrp2g4rrSfagXlLggEGRkajr_3P-o-QsNSLhYb3h8YOr9c4EneWXcT8b8g$>
These are the resources I used when I was doing constant pH MD projects. The focus of my work has changed a little and I’m afraid that these might not reflect the most up-to-date methodology in Amber to simulate titratable residues…? I hope this is still helpful to get you started on your project, and other more experienced members can educate us.
Best regards,
Amy
From: Yang, Li-Yen <zoeyxyang.gatech.edu>
Date: Tuesday, February 6, 2024 at 7:49 PM
To: He, Amy <he.1768.buckeyemail.osu.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] constant pH protonation states
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
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 Wed Feb 07 2024 - 16:30:03 PST
