RE: Protein:ligand standard binding free energies

From: Sanjay Hari (
Date: Wed Dec 11 2019 - 13:29:49 CST

I have found NAMD to be the best MD program out there, in terms of capabilities and community support. As the year comes to a close, I would like to extend a big “thank you” to both NAMD developers and the users on this list for developing and supporting this software.

From: <> On Behalf Of mohammad goodarzi
Sent: Wednesday, December 11, 2019 1:38 PM
To: Chris Chipot <>
Cc: NAMD list <>
Subject: Re: namd-l: Protein:ligand standard binding free energies


I am sorry if you got offended. You see, even your response is not constructive, If I was the author of that "tutorial", I would be asking why you think it is annoying and useless.
The simpler your protocol or whoever's protocol the better it is. When a tutorial is not well-understood, it means there is more work to be done to make it simpler.
Theory-wise it is in a great shape, but practical (i cannot even comment anymore because I feel like I am offending)

thanks for understanding and hope you see my comment as a friendly comment not a threat

On Wed, Dec 11, 2019 at 11:28 AM Chris Chipot <<>> wrote:
Hello Mo,

it is disheartening to read that you wasted three weeks of your time and
found the tutorial on protein-ligand binding "annoying" and "useless".

Perhaps can you teach everyone how to write a good tutorial, devoid of
"blah blah". Evidently, you must be an expert in the design and writing
of pedagogical material to be so openly critical.

Chris Chipot

On 12/11/19 6:12 PM, mohammad goodarzi wrote:
> 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 NAMD.
> 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
> Thanks
> Mo


Chris Chipot
CNRS research director, University of Lorraine
Adjunct professor of physics, University of Illinois, Urbana-Champaign


Chris Chipot, Ph.D.
Theoretical and Computational Biophysics Group
3161 Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
405 North Mathews
Urbana, Illinois 61801 Phone: (217) 244-4361


      It is hard for France to maintain a thirty-five-hour workweek when
      China and India have invented a thirty-five-hour workday.
                                                      Thomas L. Friedman

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