Hi Vaibhav,
You can also try the MCPB.py program to parameterize your Heme-His system: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm>.
Pengfei
> On Aug 19, 2020, at 9:56 AM, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
>
> 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
>>> _______________________________________________
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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,
>> 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
>>
>> P Please consider the environment before printing this e-mail
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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
>
> P Please consider the environment before printing this e-mail
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Sep 10 2020 - 13:30:04 PDT
