Only for binding energy concern you don't need to do separate enzyme simulation. Calculate the binding energy from your complex system. But I'll suggest you to do separate enzyme simulation for other analysis comparisons. The comparison may give you a better insight.

Thank you for the reply. Please suggest me how to do MMPBSA analysis by using the results of MD simulations run with GROMOS96 43a1 force field using prodrg toplogy files of ligand

Calculating the full thermodynamic cycle may need multiple simulations. Protein, ligand, protein+ligand unbound, and protein+ligand bound. You can use gromacs tools to set up a "disappearing act" for your ligand.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html

Or use metadynamics to "pull/push" it into or out of place.

http://www.plumed.org/

See:

http://www.mmtsb.org/workshops/Lectures/FreeEnergyMethods.pdf

Dear Sir

Thank you for the response. But I have one doubt here. It is cleared with Protein, Ligand, and Protein+Ligand bound. But confused with Protein + Ligand unbound. how to create topology files for that and do simulations. I request you to explain. I have one more question, I have enzyme docked with substrate at catalytic site. Whether MD simulation of docked enzyme substrate complex is similar to that of protein-ligand complex explained in GROMACS or should I need to do some modifications? Please clarify