[gmx-users] Ligand-protein free binding energy is become positive

masoud aliyar masoud.aliyar at gmail.com
Sat Dec 3 11:57:00 CET 2016

I’m using MM-PBSA on gromacs to calculate free binding energy of some
ligands into K-Ras (pdb-ID: 4epy). To validate MD simulation protocol and
to setup a rational threshold for evaluating the results, the co-crystal
ligand was considered as the reference ligand. Results showed that free
binding energy of reference ligand and my selected ligands have positive
quantities. Due to the fact that we are sure about the binding of reference
ligand into the binding pocket. How can we describe positive value of the
free binding energy? Results of MM-PBSA calculation for reference ligand is
as below:

Reference ligand:

van der Waal energy      =        -166.208   +/-   32.482 kJ/mol

 Electrostattic energy    =         144.473   +/-   15.430 kJ/mol

 Polar solvation energy   =         529.921   +/-   91.034 kJ/mol

 SASA energy              =         -18.937   +/-    3.458 kJ/mol

 SAV energy               =           0.000   +/-    0.000 kJ/mol

 WCA energy               =           0.000   +/-    0.000 kJ/mol

 Binding energy           =         489.143   +/-   46.438 kJ/mol

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