I am trying to differentiate between several binding poses for a protein ligand complex. Initially I tried the LIE method however its results do not followed the expected trend based on experimental data. I then looked at the raw interaction energies between the ligand and its environment (LIG-rest in g_energy). This gives better relationship but still fails to explain the experimental results. I now want to select some representative frames for analysis with external scoring functions.
I would like to select the frames that have the strongest interactions and least ligand strain. How do I obtain the internal energies for the ligand alone? (bending, twisting, stretching etc?) Also should I include the LIG-LIG LJ and Coul energies? -- View this message in context: http://gromacs.5086.n6.nabble.com/Ligand-Internal-energy-tp5000822.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
