[gmx-users] Linear Interaction energy calculations

Justin Lemkul jalemkul at vt.edu
Tue Jul 31 00:48:59 CEST 2012

On 7/30/12 5:15 PM, sai nitin wrote:
> Dear all,
> I recently started protein ligand simulation using gromacs my aim is
> to calculate binding free energies after simulations...I adapted
> justin tutorial
> and  done 10 ns MD simulations using CHARMM FF and now going through
> LIE (Linear Interaction Energie method) g_lie in gromacs..
> And came across that to perform LIE using gromacs involves two MD
> simulations one with protein - ligand simulation in solvent (which i
> finished)..and another with ligand only in solution in this step i got
> stuck can any body tell or suggest some tutorials to perform MD
> simulations for only ligand

It's nothing more than a simulation of a solute in water.  Prepare a coordinate 
file of the ligand, solvate in some suitable box, and proceed.  If you're 
already run a simulation of a protein in complex with the ligand, then you have 
the ligand's topology.  From that, construction of a .top is trivial, i.e.:

#include "whatever.ff/forcefield.itp"

#include "ligand.itp"

#include "whatever.ff/whatever_water_model.itp"

#include "whatever.ff/ions.itp"

[ system ]
ligand in water

[ molecules ]
(ions if necessary)



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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