[AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450)

From: Thirakorn Mokkawes <thirakorn.mokkawes.manchester.ac.uk>
Date: Thu, 9 Jul 2020 10:59:16 +0000

Hi,

I am new to AMBER field. I am working on P450 enzymes and attempting to study the mechanisms through Compound I.

I have the problem with generating the mol2 and frcmod files for the oxygen atom bound to Fe on heme as Compound I (Fe=O). I did the parameters files for heme and Fe, but for the oxygen should I treat it as another ligand, water, or include it in heme mol2.

I tried to follow these 2 links: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm
                                                              http://ambermd.org/tutorials/advanced/tutorial20/mcpb.htm

Another question is how to create the parameter for Cys-Fe?

Thank you in advance for any help you can offer.

Thirakorn Mokkawes (Pym)

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Received on Thu Jul 09 2020 - 04:00:03 PDT