Home » DataWarrior » Cheminformatics » Protonation state of cmpds (Any way to display if the compound is protonated or not )
Protonation state of cmpds [message #1764] Fri, 11 November 2022 02:08 Go to next message
shwang is currently offline  shwang
Messages: 1
Registered: November 2022
Junior Member
I am new to DataWarrior, and I was wondering if there is any way that it can predict the total charge of the compound or display protonated state?
Thank you.
Re: Protonation state of cmpds [message #1767 is a reply to message #1764] Fri, 11 November 2022 10:00 Go to previous message
thomas is currently offline  thomas
Messages: 666
Registered: June 2014
Senior Member
You could count the number of basic and acidic atoms, which uses a simple rule base algorithm. If you need more, you would need the capka.jar plugin (and a license for it) from ChemAxon, which DataWarrior can use to calculate pKa-values. With that you could create protonation states for any given pH value.
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