From: mohammad goodarzi (mo.goodarzi82_at_gmail.com)
Date: Wed Dec 11 2019 - 12:33:15 CST
Thanks Joao,
I am gonna watch more of the video and break down my questions so that I
get a better help.
Thanks again for your help
Mo
On Wed, Dec 11, 2019 at 11:37 AM Joao Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:
> 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--0000000000001675d5059971dd96--
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