[gmx-users] problem using g_lie

Justin Lemkul jalemkul at vt.edu
Tue Jun 4 13:40:28 CEST 2013

On 6/4/13 3:56 AM, khushboo bafna wrote:
> hii
> I ran a protein ligand simulation and only ligand simualtion in water using
> GROMACS 4.5.4
> I want to find the binding energy of the ligand and used g_lie.
> I tried to run g_lie on ligand simulation in water and got the following
> result
> Opened md_1.edr as single precision energy file
> Using the following energy terms:
> LJ:
> Coul:
> Back Off! I just backed up lie.xvg to ./#lie.xvg.3#
> Last energy frame read 2500 time 5000.000
> DGbind = -0.681 (-nan)
> Can anyone tell me what is the problem and how to go about with this

To use g_lie, you need to be analyzing an .edr file that comes from the 
protein-ligand simulation, providing the values of the ligand-water interactions 
to -Elj and -Eqq, which are simply extracted from the ligand-water .edr using 



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


More information about the gromacs.org_gmx-users mailing list