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
g_energy.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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