Protein:ligand standard binding free energies

From: mohammad goodarzi (
Date: Wed Dec 11 2019 - 11:12:13 CST

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

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
The only useful thing I found in that tutorial was figure page 9.

So my question is that is there any tutorial that shows steps by step how
to make the input and run NAMD for such calculations?

Sorry again if this is naive question but after 3 weeks wasting my time on
the above tutorial, I cannot even understand why they put such blah blah in
their website


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