Article ID: 636 - Last Modified: May 16, 2011
Is there any way to change the protonation states for residues in the active site when preparing the Glide grid? For example, if I want to have a tyrosine in a deprotonated state, how should I do this?
The H-bond assignment step of the Protein Preparation Wizard (PPW) changes GLU/ASP protonation states and HIS protonation/tautomer states in order to maximize the H-bond network. However, you will have to deprotonate TYR manually. This can be done while running the Protein Preparation Wizard. You should do it before the "Generate Het States" step, since the het states you choose might be influenced by the protonation states of active site residues.
The easiest way to deprotonate TYR is to decrease the oxygen formal charge to -1 using the Build toolbar. This will automatically remove the hydrogen, too. If you delete the hydrogen and then decrease the oxygen charge, you will have to refresh the PPW by clicking "Analyze Only".
Keywords: protonation states, H-bond assignment, tyrosine, PPW, active site protonation states, deprotonate TYR
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