[AMBER] Constant pH MD Simulation

From: Dulal Mondal via AMBER <amber.ambermd.org>
Date: Fri, 29 Jul 2022 12:58:41 +0530

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
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Received on Thu Aug 04 2022 - 13:37:36 PDT
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