Binding sites along with binding energy can be easily determined using ADT. However, MD simulations have been reported by researchers using Schrodinger Desmond. So I was wondering if there is a possibility of carrying out MD simulations using ADT and generating RMSD curves/plots.
From my experience, I would say no because Autodock Tools is not equipped for molecular dynamics (MD) simulations.
I don't know where you read such a thing (could you provide the reference?), but probably they used Vina for docking and subsequently performed a MD simulations with a specific software, like the Schrödinger Desmond you said.
Remember that Vina and Autodock Tools are primarily designed for molecular docking studies. If you're interested in MD simulations and RMSD analysis, you would need to use dedicated MD simulation software such as Schrödinger Desmond, GROMACS, AMBER, or NAMD.
Using the MD software, you can perform simulations and then analyze the resulting trajectories to obtain RMSD data.
Thanks Davide Pietrafesa for your elaborate explanation.
AutoDock Vina is primarily designed for molecular docking simulations, which focus on predicting the binding modes and affinities of ligands with a target protein. AutoDock does not perform molecular dynamics simulations on its own. Other tools like GROMACS, AMBER, or NAMD can be used to analyze the dynamics of a system and obtain root mean square deviation (RMSD) curves.
Thanks C. K Biju for the explanation and I appreciate your insights.
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