ADL: Protonation states

Collignon, Barbara C. collignonbc at
Thu Oct 1 13:36:05 PDT 2009

Dear all,

Could someone please explain how Autodock choose protonation states ?

From: autodock-bounces at [autodock-bounces at] On Behalf Of Song Yunfeng [syf8728 at]
Sent: Tuesday, September 29, 2009 9:18 PM
To: autodock at
Subject: ADL: deal with Asp/Glu/His

Dear autodockers:
Before we dock a ligand and a protein, how to deal with the amino acid Asp/Glu/His. Need we add protonation to them?


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