You might find the methodology of Shahrokh et al. for importing/using HEME
parameters in tleap useful.
https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21922
On Tue, Aug 18, 2020 at 9:40 PM Mohamed M. Aboelnga <
mohamedm.aboelnga.mail.concordia.ca> wrote:
> Hello Pengfei,
>
> I tried to follow your suggestion to have the bound oxygen to the Fe as an
> independent residue but I am not able to parameterize it. Once I use
> antechamber it gives an error saying "ERROR in xmin(): Too few atoms.". Let
> me know if I understood your suggestion properly and if there is anything
> else I should do!
>
> Many thanks for your endless support!
>
>
> Sincerely,
> Mohamed M. Aboelnga, PhD
> Horizon Postdoctoral Fellow
> Centre for Research in Molecular Modeling (CERMM)
> Department of Chemistry and Biochemistry
> Concordia University, Montreal, Quebec, CANADA
>
> ________________________________
> From: Pengfei Li <ambermailpengfei.gmail.com>
> Sent: July 20, 2020 11:53 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I
> (heme enzyme, P450)
>
> Hi Thirakorn,
>
> > On Jul 9, 2020, at 6:59 AM, Thirakorn Mokkawes <
> thirakorn.mokkawes.manchester.ac.uk> wrote:
> >
> > 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.
> >
>
> You should treat the oxygen as an independent residue from Fe.
>
> > 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?
> >
>
> MCPB.py can handle this case, it will recognize the CYM/CYS residue
> automatically as long as your PDB file is consistent with AMBER naming
> scheme for amino acids (but you need to make sure the cysteine residue has
> the correct protonation state).
>
> > Thank you in advance for any help you can offer.
> >
>
> Pengfei
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>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
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Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
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Received on Tue Aug 18 2020 - 23:30:02 PDT
