Re: Protein:ligand standard binding free energies

From: mohammad goodarzi (mo.goodarzi82_at_gmail.com)
Date: Wed Dec 11 2019 - 12:37:52 CST

Chris,

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
Mo
Mo

On Wed, Dec 11, 2019 at 11:28 AM Chris Chipot <chipot_at_ks.uiuc.edu> 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
> >
> 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.
> > 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
>
> E-mail: chipot_at_ks.uiuc.edu
> Christophe.Chipot_at_Univ-Lorraine.fr
> Web: http://www.ks.uiuc.edu/~chipot
> http://www.lia-uiuc.cnrs.fr
>
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> _______________________________________________________________________
>
>

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