Re: [AMBER] Constant pH MD Simulation

From: Adrian Roitberg via AMBER <>
Date: Fri, 29 Jul 2022 11:50:37 -0400

I am not sure what you mean by "How can I find a deprotonated state for LYS"

To find out the parameters, there is a residue named LYN which
represents the deprotonated state of a LYS. The deprotonated state of
LYS under constant pH conditions should mimic that residue in terms of

Do you want to know how often LYS is deprotonated during a cpH MD ? should tell you that.


On 7/29/22 3:28 AM, Dulal Mondal via AMBER wrote:
> [External Email]
> Dear Sir/Madam
> I am running CpHMD Simulation. As has been stated in the tutorial by
> default, all protonation states start at state 0. We also know the default
> protonation for each of the titratable residues. When AS4 and GL4 use
> deprotonated form by default, TYR, LYS and CYS start from the singly
> protonated states. Whereas, for TYR and CYS the default protonation is
> understandable from the population chart, I am unable to understand what 3
> stands for LYS ( at state 0). How can I find a deprotonated state for LYS.
> Any help will be appreciated.
> With regards
> Dulal Mondal
> _______________________________________________
> AMBER mailing list

Dr. Adrian E. Roitberg (he/him/el)
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
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Received on Thu Aug 04 2022 - 13:37:41 PDT
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