On Fri, Apr 09, 2021, A R wrote:
>
>I have an inhibitor ligand that interact covalently linked with the protein.
>The free ligand has propargyl fragment that is responsible for bonding to
>the protein through addition reaction on the triple bond.
>
>How I prepare starting coordinates and topology files using tleap and at
>same time consider this type of covalent bonding interaction between ligand
>and protein.
This is indeed an advanced type of problem. The approach I would take is to
create a modified residue that contains the proper covalent linkage.
Tutorial 5.3 is pretty close to what you want to do, so start with that.
But that is a fairly complex chromophore (for green fluorescent protein).
I'm hoping we can get someone to donate or create another amino acid
modification tutorial soon.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 09 2021 - 18:30:02 PDT
