Dear Wu,
In your original pdb file, you do not need to rename the MET (which coordinates to Mg2+) to a different residue name because when MET coordinated to the metal ion, it does not lose any protons. This is different from CYS that when it coordinates to a metal ion it may lose a proton, if it loses a proton, then the residue name should be CYM instead of CYS based on AMBER naming scheme.
Thanks for Vaibhav’s detailed response. Yes, the metal coordinating residues will be renamed by MCPB.py during the MCPB.py modeling in order to differentiate them from other residues because they have different parameters.
Pengfei
> On Oct 28, 2020, at 9:41 PM, Wu Xu <wu.xu.louisiana.edu> wrote:
>
> Dear Vaibhav,
>
> Thank you for the comments. I was able to follow all steps of CYM-HEME in this tutorial as well. I can try HID-MG-chlorophyll first rather than MET-MG-chlorophyll.
>
> Best,
>
> Wu
>
> ________________________________
> From: Vaibhav Dixit <vaibhavadixit.gmail.com>
> Sent: Wednesday, October 28, 2020 7:31 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] a metal bound Met
>
> Dear Wu,
> I have run this tutorial successfully and also modified it successfully for
> Heme proteins with His ligands.
> Thus, you might find my following comments useful.
>
> 1) Although the residue is renamed CYM, in the beginning of the tutorial,
> it is later called "CM1" which is also the name of the mol2 file for the
> modified CYS.
> 2) This CM1 residue doesn't contain the SH proton (atom type HG), which was
> deleted manually from the pdb (Protein_H.pdb).
> 3) The final pdb 4ZF6_mcpbpy.pdb, also contains CM1 residue name instead of
> CYM.
> 4) In short the residue name in all mol2 files (with charges) for
> non-standard residues should match those in the final pdb used for creating
> prmtop/inpcrd files, else leap will complain about new atom-types and
> missing parameters (unless they happen to luckily match with standard ones,
> which is rare for non-standard systems).
> 5) The MCBP.py script seems to handle these changes well, nonetheless one
> should manually check all output files at each of the steps especially
> while building parameters for a new non-standard system.
> 6) In the case of Heme-HIS protein the coordinating HIS residue was renamed
> as HD1 by the script and I had a corresponding HD1.mol2 file.
>
> I hope this helps.
>
> On Thu, Oct 29, 2020 at 1:03 AM Wu Xu <wu.xu.louisiana.edu> wrote:
>
>> Dear Amber user,
>>
>> I am trying to create .prmtop .inpcrd for a ligand-bound protein where a
>> Met residue is coordinated to Mg of chlorophyll
>>
>> I am following the tutorial
>> https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.php
>> In this tutorial, a Cys residue is bound to Heme through Fe. CYS was
>> renamed as CYM because of metal ion binding of CYS.
>>
>> My question: Is there a name for Met when it binds a metal ion similar to
>> CYS-CYM situation? If not, how to handle Met-Mg-chlorophyll situation?
>>
>> Thanks,
>>
>> Wu
>>
>>
>> Dr. Wu Xu
>>
>> Professor of Biochemistry
>>
>> Department of Chemistry
>>
>> Room No. 138, Montgomery Hall
>>
>> 300 E. St. Mary BLVD
>>
>> P.O. Box 43700
>>
>> University of Louisiana at Lafayette
>>
>> Lafayette, LA 70504
>>
>> Telephone: 337-482-5684 (office)
>>
>> 337-482-6739 (lab)
>>
>> Fax: 337-482-5676
>>
>> Email: wxx6941.louisiana.edu<mailto:wxx6941.louisiana.edu>
>>
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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,
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> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
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>
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>
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>
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Received on Fri Nov 20 2020 - 07:30:03 PST
