Hi Mohamed,
Sorry for the late reply. I am busy with preparing a class for this semester.
You can use the metalpdb2mol2.py script that was mentioned in and can be accessed through this webpage: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm>.
Pengfei
> On Aug 18, 2020, at 12:10 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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Received on Thu Sep 10 2020 - 13:30:03 PDT
