Re: Protein:ligand standard binding free energies

Date: Thu Dec 12 2019 - 03:50:46 CST

Dear Mo,

Although I am far from being qualified to address your issue here and also to defend the tutorial from your critical comment, as I am also a beginner in this vast field. But reading an another mail of yours where you are asking for an error of parameters, which make me think that you are at very beginner level of MD simulation with NAMD and not at all thorough in basics.
And then you are attempting a tutorial (protein-ligand free energy) which is a advanced tutorial, and require you to be thorough in theoretical underpinnings as well and alot more.

So it is very irresponsible of you to make such a comment, as being critical is not a wrong thing, but first put some efforts to become qualified, to criticize.

And let me clarify that I am also one of a beginner users of namd and vmd, and I can say that it requires efforts to even learn these things, so must have taken much much efforts to develop these programs and tutorials, so atleast respect that effort.

In the end, I am sorry if I am being judgemental, but I can't stop myself writing to you after reading your mail, because I always got a helping hand here, no matter how novice or crude my question is.


From: <> on behalf of mohammad goodarzi <>
Sent: Wednesday, December 11, 2019 10:42 PM
To: NAMD list <>
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

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


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