Damn I meant pka_corr=0.0
-----Message d'origine-----
De : Feng, Zimin
Envoyé : 1 mars 2019 15:33
À : 'AMBER Mailing List'
Objet : RE: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid?
I meant pka=0 -> NHE here :P
-----Message d'origine-----
De : Feng, Zimin
Envoyé : 1 mars 2019 15:29
À : AMBER Mailing List
Objet : RE: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid?
Hi Vinícius,
Thank you so much.
So the 0 in titratable_residues.py of HEH entry refers to NHE. If I place another redox-active residue in it, I need to align it with NHE as well. Got it! I was thinking it wrong :P
Warmest regards,
Zimin
-----Message d'origine-----
De : Cruzeiro,Vinicius Wilian D [mailto:vwcruzeiro.ufl.edu]
Envoyé : 1 mars 2019 15:01
À : AMBER Mailing List
Objet : Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid?
Courriel provenant de l'externe
ATTENTION, avant d'accéder à une pièce jointe ou à un lien de ce courriel, assurez-vous que celui-ci provient d'un tiers de confiance.
Hello Zimin,
Correct, only the relative reference energies matter. Thus, the reference energies could be any values, as long as the differences between them are the same. Each titratable residue has its own set of reference energy values (both pH- or redox-active residues): one reference energy per protonation or redox state. The procedure to obtain reference energies for redox-active residues is the same as for pH-active residues: assuming you have two states (oxidized and reduced) you may fix the reference energy as 0 for one of the states, and then fit the other value based on the standard redox potential value for the reference compound (for more details see https://aip.scitation.org/doi/full/10.1063/1.5027379 ).
Even though there is an expression for the redox potential in terms of the concentration of e- (see the paragraph between equations 1 and 2 of the paper above), equivalent to the pH expression as a function of H+, the redox potential value you consider in the simulations can be shifted according to a given reference. As long as you use the same reference during the reference energy calculations and during the production simulation afterward (for all redox-active titratable residues in your simulation), then you are fine. In the paper mentioned, the reference used for the redox potential was vs. NHE, however, any other could have been chosen.
Please let me know if you have any questions further,
All the best,
Vinícius Wilian D. Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Feng, Zimin <Feng.Zimin.hydro.qc.ca>
Sent: Friday, March 1, 2019 10:47 AM
To: AMBER Mailing List
Subject: Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid?
Thank you very much Vinícius!
It's a great honor to hear from the creator of the program himself :-)
One more question: in CpH or constant redox potential reference energies, it is only the difference between ref energies that matters, right? So that all of them has one state's energy set to 0. But when we have multiple titratable residues or multiple redox centers, where we would like to find the relative redox potential (e.g., THF vs metallic lithium or vs standard hydrogen electrode), is it still safe to assign a 0 to each and every one of the residues where redox reactions could take place?
In one of the CpH tutorials it did this, but pH has an absolute meaning as the concentration of H+ while redox potential doesn't, unless we assume a common reference like standard hydrogen electrode, bromine electrode etc.. Does that mean, if we want to find ref energies with finddgref.py, we should put two residues together and find the energy between the one where one (standard) residue is 50% reduced and the one where the (measured) residue is 50% reduced? Intuitively this determines the difference between the mid-values of the redox ref states of respective residues ( (E_1_std + E_2_std)/2 vs. (E_1_new + E_2_new)/2 ), and then we have some sort of freedom to choose the values of E_1_std and E_1_new, but not E_1 and E_2?
I'm not sure if I made the right claims here and I think it's a good idea to hear your opinion :-)
With warmest regards,
Zimin
-----Message d'origine-----
De : Cruzeiro,Vinicius Wilian D [mailto:vwcruzeiro.ufl.edu]
Envoyé : 27 février 2019 17:42
À : AMBER Mailing List
Objet : Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid?
Courriel provenant de l'externe
ATTENTION, avant d'accéder à une pièce jointe ou à un lien de ce courriel, assurez-vous que celui-ci provient d'un tiers de confiance.
Hello Zimin,
Through the command "cpinutil.py --describe" you are able to access the full list of reference energies currently in the Amber library. There are residues in the library (like AS4, for example) with reference energies in the same range as yours.
finddgref.py is sort of a "fail safe" tool because its predictions come directly from the constant pH output(s) file(s) produced in the simulations. In the serial mode, for example, finddgref.py would only stop when the fraction of protonated species for a given residue is sufficiently close to 50% at the pH you set. Please bare in mind that your reference energy depends not only on the charge distributions you set for each protonation state, but also on your solvent model and igb choices. Other than that, as long as your initial structure is properly equilibrated and your simulation parameters are correct in your mdin file (make sure your MD simulations are long enough to ensure the fractions you are obtaining are converged), you should be fine.
I hope this helps,
Best,
Vinícius Wilian D. Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Feng, Zimin <Feng.Zimin.hydro.qc.ca>
Sent: Wednesday, February 27, 2019 3:25 PM
To: AMBER Mailing List
Subject: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid?
Dear AMBER community,
I have a question about the value of dG_ref for the constant pH MD.
Basically I was using finddgref.py to get the reference energy (deprotonated state was set to 0 energy so this will be the energy difference as well) for acetic acid CH3COOH. I got a seemingly big value as 34 kcal/mol or ~1.5 eV.
I'm new to AMBER and I wonder if this number is reasonable or not? During the calculation no error messages was shown but the result seems a lot bigger than what the other titratable residues have.
Any comments will be appreciated and I thank you in advance!
Zimin
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Received on Fri Mar 01 2019 - 13:00:04 PST
