AMBER Archive (2009)

Subject: [AMBER] Zinc ion, help

From: Mahmoud A. A. Ibrahim (
Date: Tue Jul 07 2009 - 09:26:48 CDT

Dear AMBER Users
I am working on metalloproteins (MMP) and they have Zinc ion in its active site. As you know, Zinc ion parameter is a problem. In the following paper:

the author derived the partial charges depending on a model of Zinc ion with three methylimidazoles and one acetate ion. The three imidazoles here take place of three histidine residues in the active site.
Sorry, I am a little confused. According to AMBER manual, we should cap the cut-off residues with NME or ACE in order to maintain the overall charge, i.e. each histidine residue should be capped with two NME (or ACE). By this, three imidazoles model will not give an accurate charge.
Am I right? I am so sorry, I feel I misunderstand something. I need a help, please.
Thanks in Advance
M. Ibrahim

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