I'm also planning to generate similar parameters for Heme-His system.
This would need, I guess, generating a new residue for His bound to Heme
(e.g. HIH)
But I suspect that other users on the list might have already done this.
I hope they would respond and share their experience here.
On Wed, Aug 19, 2020 at 6:51 PM Mohamed M. Aboelnga <
mohamedm.aboelnga.mail.concordia.ca> wrote:
> Thanks for sharing this paper.
>
> I had read it before but preferred to use the bonded model to
> parameterize my heme and have full control on the settings specially mine
> has a His-Fe bond unlike P450.
>
> In fact, I have used the MCPB tutorial successfully to parameterize the
> resting state heme and used the generated parameters for numerous MD
> simulations. Now, I only need to know how to use it properly for compound I
> instead!
>
> 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: Vaibhav Dixit <vaibhavadixit.gmail.com>
> Sent: August 19, 2020 12:11 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)
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
>
> 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,
> Department of Pharmacy,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
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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,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Wed Aug 19 2020 - 07:00:02 PDT
