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

Protonation state of cmpds [message #1764]

Fri, 11 November 2022 02:08

shwang
Messages: 1
Registered: November 2022

Junior Member

Hi,
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.

Report message to a moderator

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

Fri, 11 November 2022 10:00

thomas
Messages: 736
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

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: Tue Oct 28 10:37:55 CET 2025

Total time taken to generate the page: 0.62185 seconds