Protonate/Deprotonate Compounds
Protonate/deprotonate compounds per a given pH, in preparation for docking.
Menu: Compounds → Build → Compound Protonation
Guided tour: Launch in MolModa
This plugin uses the Open Babel library to guess at proper protonation states.
Where to find it
Dialog
Parameters
| Parameter | Default | Description |
|---|---|---|
makemolinputparams |
— | — |
| Protonation pH | 7.4 |
Physiological pH is 7.4. |
| Regenerate 3D coordinates | none |
Whether to regenerate 3D atomic coordinates given the new protonation state. |