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 Mon Sep 23 2024 - 20:00:02 PDT
