AMBER Archive (2009)

Subject: [AMBER] Metalloproteins - Ligand Protonation

From: s. Bill (
Date: Fri Jul 31 2009 - 13:01:42 CDT


I hope to find anybody worked before on Metalloprotiens.

I am working on simulation of MMP-3 inhibited with Hydroxamate ligand (CH3-C(O)-N(H)-OH).

I would like to enquire about the protonation state of Hydroxamate
inside the protein, when I build the ligand, which state should I use
for the ligand, protonated or not?

I am really confused, and no paper mentioned this issue.

Thanks in advance


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