AMBER Archive (2009)

Subject: [AMBER] Protonated or not

From: s. Bill (
Date: Fri Jul 31 2009 - 12:15:32 CDT

I am just a little confused about the protonation state of Hydroxamate (inhibitor). Its pKa ranging between 8.4 and 9.1. Does it mean, it should be protonated (in its acidic form) during the simulation which run at pH 7.
I am so sorry, I got confused from the papers, it called the protonated form (sometimes) hydroxamate (it should be called Hyroxamic).
Thanks in advance

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