Re: Fwd: FEP protein-ligand tutorial 2017 unclear section

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon May 07 2018 - 08:03:34 CDT

Thanks. I could now deal also with the analysis of restraint TI.

Saying sorry for my overlooking of what was described in the tutorial is an
understatement.
I can't explain how it happened but, most unfortunately for all, it
happened.

francesco

On Sat, May 5, 2018 at 4:28 PM, Chris Chipot <chipot_at_ks.uiuc.edu> wrote:

> Let me, please, add my two cents here, starting with agreeing
> wholeheartedly with Giacomo's message.
>
> As indicated in section 2 of the tutorial,
>
> For each value of lambdaSchedule and for each collective variable, dG/dλ
> is computed. The free-energy contribution due to the restraint of interest
> is obtained by integrating the gradient profile.
>
> As for collecting the gradients, it is indicated in section 3 of the
> tutorial,
>
> grep "dA/dLambda" rest-01.log
>
> Suffice, as JC suggests it, to pipe the latter with awk to extract the
> relevant information, and,
>
> integrate the gradients, using for instance XMGrace to recover the
> associated free-energy profile
>
> From a broader perspective, while the authors of the tutorials, who work
> on their free time to offer a service to the community, welcome
> constructive comments aimed at improving their text, completion of the
> tutorials requires a minimum effort from the users, which includes reading
> the literature and getting familiarized with the different concepts at
> hand. It would also be foolish to start with the protein-ligand tutorial if
> completely unfamiliar with free-energy calculations. More basic tutorials
> are available.
>
>
> Chris Chipot
>
>
> On 5/5/18 2:20 PM, JC Gumbart wrote:
>
> How could ParseFEP deal with the restraints? Even the ghost ligand in
> Alchemy:Bound is still being held to the binding site. If you haven’t read
> the source paper yet https://www.ncbi.nlm.nih.gov/pubmed/23794960
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pubmed_23794960&d=DwMFaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=9wcx8ZVYDU3cBjfC5XwhAmBCQ4x0JWmwYlnc1qYwLxE&s=fEc3SrNF7drTHhNqidFd_IdmcUFNUiGKc344tOOVk5o&e=> ,
> it might help with the logic behind the different steps.
>
> I don’t remember the exact format of the output, but I imagine grep +
> awk/sed will extract the relevant lines.
>
> Best,
> JC
>
>
>
> --
>
> 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
> 3165 Beckman Institute for Advanced Science and Technology
> University of Illinois at Urbana-Champaign
> 405 North Mathews
> Urbana, Illinois 61801 Phone: (217) 300-0380
>
> 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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> Thomas L. Friedman
> _______________________________________________________________________
>
>

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