Proceed with molecular docking using preferred tool and then go for MDS.

Bahare Khoshkholgh :

The protein structure obtained with AlphaFold would already be optimized with respect to its geometry. However, to use this predicted structure as a docking target, you could consider using a force-field method for optimizing the hydrogen-bonding network. In addition, note that OpenBabel is not designed for optimizing the geometry of a protein.

For the ligand(s), it is good practice to do a geometry optimization with a force-field method to help ensure that you are starting with structures that have correct bond lengths and bond angles. QM methods could also be used, but these are time-consuming an usually not necessary as a prelude to docking.

To carry out the docking itself, use software that is designed for this purpose. MD simulations are not designed for docking simulations. However, after you have obtained protein-ligand complexes from docking, you could carry out MD simulations on the complexes in order to study, for example, the stability of the complexes or the effects of ligand binding on protein flexibility.

You may follow these steps to initiate Protein-Ligand Docking in MD Simulation:

First perform docking using any of the following - Glide by Schrodinger, Autodock, Flare Pro+ etc.

Then perform MD Simulation for the docked protein-ligand complex using suitable MD package & force field like AMBER, Desmond, Gromacs, NMD etc.

Then you can analyze the MD simulation results in terms of their RMSD, RMSF, Radius of Gyration, MM-GBSA etc.

Hope it gives an idea to start :)

First of all, before going towards MD Simulation, you need to Dock your protein with a specific ligand with a protein of interest via Vina, Autodock, etc. After that, you make complexes and go through the process of preprocessing your Complexes and making them ready for MD Simulation via Amber, GROMACS, etc.

If you have any more questions, feel free to ask.

Thank you

First of all, before going towards MD Simulation, you need to Dock your protein with a specific ligand with a protein of interest via Vina, Autodock, etc. After that, you make complexes and go through the process of preprocessing your Complexes and making them ready for MD Simulation via Amber, GROMACS, etc.

If you have any more questions, feel free to ask.

Thank you

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