Protein-ligand complex

From: Raman Preet Singh (
Date: Tue Jun 23 2020 - 08:47:56 CDT

Dear All,

I am looking to simulate an enzyme-inhibitor complex. PDB contains a structure of enzyme+cofactor+inhibitor. I would like to replace the inhibitor in the PDB crystal structure with my inhibitor molecule and perform MD.

I have performed docking using AutoDock Vina and would now like to perform MD of the complex (enzyme+cofactor+my inhibitor). Is there any step by step tutorial available to perform the following steps:
1. parameterize the cofactor and my inhibitor
2. combine the cofactor and inhibitor with the enzyme


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