Re: [AMBER] Question about the use of MCPB.py(Handling of proteins with non-standard residues in the chain) from Li, Zhen via AMBER on 2024-09-25 (Amber Archive Sep 2024)

From: Li, Zhen via AMBER <amber.ambermd.org>
Date: Thu, 26 Sep 2024 03:06:30 +0000

Hi Yifei,

Thank you for being interested in MCPB.py. I have encountered a similar question before: “What if the metal center has a non-standard residue coordinating with it?”

The short answer is “customize this KCX residue and then feed the frcmod plus mol2 parameters to both MCPB.py’s and tleap’s input files”.

I agree that it is hard to do so, and the best tutorial that I can find is here<https://carlosramosg.com/amber-custom-residue-parameterization> for generating FRCMOD and here<https://pablito-playground.readthedocs.io/en/latest/tutorials/qmmm_amber_cpmd/mol2_file.html> for generating MOL2.

The FRCMOD generation already considered that the residue is linked to the main chain, while the MOL2 tutorial does not. This should be fine since linking to the main chain will not affect the MOL2 charge a lot, and the model will be sent to QM calculations anyway.

If all the attempts still fail. Please feel free to go with the QM/MM option. QUICK now supports many basis sets and functionals for transition metals.

I will be working on a tutorial about “MCPB.py with modified residue” soon.

Wish all the best.
Zhen.
>
> On Sep 23, 2024, at 10:31 PM, 郑逸非 via AMBER <amber.ambermd.org> wrote:
>
> Hello!
>
> I'm new to AMBER. I would like to know if it is possible to use MCPB.py for proteins containing nickel metal ions in the active site with non-standard residues in the backbone.
>
> Both examples “Building Bonded Model for A Ligand Binding Metalloprotein with MCPB.py” and “Building Bonded Model for A HEME Group with MCPB.py” are tutorials that deal with ligand molecules, metal ions, and water molecules independent of proteins. It doesn't seem to be possible to use the methods of the first two examples to work with structured molecule files. My question is what should I do when I encounter a structure that contains non-standard residues in the main chain with a metal site(PDB code:4CEU)?  There is a LYSINE NZ-CARBOXYLIC ACID(KCX) in subunit α. Should I just replace it with lysine or is there another way? Any tutorials or simple steps to share? Thank you!
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Received on Wed Sep 25 2024 - 20:30:02 PDT