[gmx-users] how to obtain binding energy?

Justin A. Lemkul jalemkul at vt.edu
Tue May 17 15:32:45 CEST 2011

mohsen ramezanpour wrote:
> Dear Shahab
> Yes,when you compute delta Gibbs energy of binding ,You can compute 
> binding constant(Kd or Ki)
> by thermodynamics relations as Dr.Justin said.
> I think both methods can be applied to any systems which you wish to 
> have its binding free energy.
> (including protein-protein,protein-ligand ,protein-Nucleic Asids and 
> ligand-Nucleic asids)

True, but you will probably get bad convergence for TI with large molecules, 
especially those that are not net neutral (like nucleic acids and most 
proteins).  PMF is much easier in this case, and probably more reliable.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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