[gmx-users] LINEAR INTERACTION ENERGY

[Vytautas Rakeviius]

You need separate energygrps (http://manual.gromacs.org/online/mdp_opt.html (output control) for all average components in LIE equation: Protein, Ligand and solvent.Probably you will need "gmx energy" too to extract average Ligand-solvent interaction terms from edr file before inserting them into "gmx lie".And make sure you know LIE equation, check that paper I gave you or references about LIE inside it.
 

    On Thursday, March 16, 2017 1:26 PM, Kulkarni R <alumniphysics at hotmail.com> wrote:
 

 
Thanks.


You have mentioned "proper energy groups" in mdp file


Could you please say more about it?


Thanks,

Kulkarni.R

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Vytautas Rakeviius <vytautas1987 at yahoo.com>
Sent: Thursday, March 16, 2017 10:29 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] LINEAR INTERACTION ENERGY

Basically you do two MD runs one with ligand in water other with ligand in protein. You must set proper energygrps in mdp file so you get 2 edr files from runs and in the end you use "gmx lie" (http://manual.gromacs.org/programs/gmx-lie.html) to compute difference between those two edr files.You might check this paper too:
gmx lie - GROMACS<http://manual.gromacs.org/programs/gmx-lie.html>
manual.gromacs.org
Synopsis gmx lie [-f [.edr>]] [-o [.xvg>]] [-nice ] [-b ] [-e ] [-dt ] [-[no]w] [-xvg ] [-Elj ] [-Eqq ] [-Clj ] [-Cqq ] [-ligand ]


Curr Comput Aided Drug Des. 2015;11(3):237-44.

    On Thursday, March 16, 2017 12:15 PM, Kulkarni R <alumniphysics at hotmail.com> wrote:


 Hi gromacs users,

In order to calculate delta G (Gibbs free energy) for protein ligand binding, what are the steps to be followed in Linear interaction energy?


Are there any tutorials for the same?


Thanks,

Kulkarni.R
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