[gmx-users] delta G of binding for protein-ligand complex

[Archana Sonawani]

Dear Gromacs Users,

I have two large organic compounds and one peptidomimetic binding to same
receptor protein. I want to compare the delatG of binding of all the three
complexes to show that peptidomimetic binds with greater affinity to
protein. According to the gromacs tutorial,  I have to perform (de)coupling
of the ligand in complex with the receptor and in bulk solution. I don't
know exactly how to start with this process.

Do I need only the protein-ligand complex simulated for 5ns to start with?

Thanks in advance.
-- 
Archana Sonawani-Jagtap
Junior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339