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

From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Sat May 05 2018 - 09:28:27 CDT

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
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                              E-mail: chipot_at_ks.uiuc.edu
                                      Christophe.Chipot_at_Univ-Lorraine.fr
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