[AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme) using MCPB tool

From: Mohamed M. Aboelnga <mohamedm.aboelnga.mail.concordia.ca>
Date: Sun, 23 Aug 2020 15:31:58 +0000


I have used MCPB tool to parameterize my heme in presence of ligand but I could not use the same tool to parameterize it in the form of compound I where there is a bound oxygen to the iron center! I tried to treat this oxygen as a separate ligand but encountered errors in its parameterization.

If any one could provide my with a solution or suggest a more appropiate way to handle it it will be much appreciated.

Mohamed M. Aboelnga, PhD
Horizon Postdoctoral Fellow
Centre for Research in Molecular Modeling (CERMM)
Department of Chemistry and Biochemistry
Concordia University, Montreal, Quebec, CANADA

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Received on Sun Aug 23 2020 - 09:00:03 PDT
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