From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Wed Dec 11 2019 - 11:37:58 CST
Dear Mohammad,
Did you read the box with a skull on page 4 saying: “This tutorial contains advanced material. Do not attempt to tackle the problems therein if you have no preliminary experience with free-energy calculations. The neophyte reader eager to get acquainted with the computation of protein:ligand standard binding affinities is advised to complete first the introductory tutorials on alchemical, free-energy perturbation calculations and adaptive-biasing-force calculations.”
If you are not comfortable with NAMD simulations, how to prepare the structure, the configuration files, and supporting files, please take a look at the NAMD tutorial: https://www.ks.uiuc.edu/Training/Tutorials/#namd. If you are familiar, there are other tutorials that you should go through- https://www.ks.uiuc.edu/Training/Tutorials/#fep to be adequately trained in this type of methodology. Bear in mind that free-energy simulations are not as simple as many try to paint it.
Also, we have the lectures of our workshops stored on our youtube channel that you can watch - https://www.youtube.com/watch?v=3hCaeFF05Jc&list=PL8XC6Vx8S1GDuJtKeIe8muGmQURVQnl_m.
I hope this can help you.
Best,
João
From: <owner-namd-l_at_ks.uiuc.edu> on behalf of mohammad goodarzi <mo.goodarzi82_at_gmail.com>
Reply-To: <namd-l_at_ks.uiuc.edu>, mohammad goodarzi <mo.goodarzi82_at_gmail.com>
Date: Wednesday, December 11, 2019 at 11:17 AM
To: NAMD list <namd-l_at_ks.uiuc.edu>
Subject: namd-l: Protein:ligand standard binding free energies
Hello everyone,
I am sorry if this email bother you but seriously I found it very annoying tutorial and useless which led me to nothing. Either I am looking at wrong thing or I am doing something wrong. I just want to get to the right path. I am reading this tutorial
http://www.ks.uiuc.edu/Training/Tutorials/namd/PLB/tutorial-protein-ligand.pdf
I have a protein and a ligand and I have done docking already. now I want to make a better estimate of the binding, so I am thinking to do MD with NAMD--B_3658909078_2060406968--
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