How to perform Molecular dynamics simulation of metallo-protein using CHARMM36ff in gromacs??

30 August 2024 1 8K Report

There is a cobalt in active site of protein, I want to use CHARMM36 ff in gromacs I'm no getting how to start. Can anyone suggest me any tutorials or documentation should I follow for performing MDS of metallo-protein with ligand. thank you!

Arpit Jain

Prepare Protein: Add cobalt to the active site.

Generate Topology: Use pdb2gmx with CHARMM36, customize for cobalt.

Ligand: Assign topology using CGenFF.

Solvate: Use TIP3P water model.

Set Simulation: Define temperature, pressure, and simulation parameters.

All of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.

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