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

Archana Sonawani ask.archana at gmail.com
Fri Oct 12 11:44:57 CEST 2012

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,
Mumbai, India.

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