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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.