openmolecules.org Forum: Cheminformatics » Protonation state of cmpds

Home » DataWarrior » Cheminformatics » Protonation state of cmpds (Any way to display if the compound is protonated or not )

Show: Today's Messages :: Polls :: Message Navigator

Re: Protonation state of cmpds [message #1767 is a reply to message #1764]

Fri, 11 November 2022 10:00

thomas
Messages: 715
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.

Report message to a moderator

[Message index]

		Protonation state of cmpds By: shwang on Fri, 11 November 2022 02:08
		Re: Protonation state of cmpds By: thomas on Fri, 11 November 2022 10:00

Previous Topic:	Add pharmacophores into the 3D-view ?
Next Topic:	Optional automatic protonation feature of Nitrogen in DW using EL

Goto Forum:

-=] Back to Top [=-

[ Syndicate this forum (XML) ] [

] [

]

Current Time: Thu Nov 21 23:10:02 CET 2024

Total time taken to generate the page: 0.03649 seconds