As I say continually, I am not a private tutor. Please keep all Gromacs-related
correspondence on the gmx-users list. I am CC'ing this message there and would
ask that any further discussion be held in this forum.
Binding energy is not trivial to calculate, and will require some type of free
energy calculation (thermodynamic cycles, potential of mean force, etc).
Breakdown of short-range nonbonded terms can be accomplished by using the
"energygrps" keyword in the .mdp file. If you've already done your simulation,
you'll have to use the mdrun -rerun function with a new .tpr file that has these
groups defined.
-Justin
rajender verma wrote:
dear sir
I have done MD study of a complex compound (protein-Ligand). I want to
calculate the Binding and breakdown energy with protein- ligand. pllease
help me sir
Thanks
--
Rajender Kumar
Senior Research Fellow
National Institute of Pharmaceutical Education and Research (NIPER),
Sector - 67, S.A.S. Nagar. 160062, Punjab, INDIA
http://bioinfoindia.weebly.com/
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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