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,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
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https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
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Received on Wed Oct 28 2020 - 19:00:02 PDT
