[gmx-users] Ligand Internal energy

Tom Dupree t.dupree at unsw.edu.au
Thu Sep 6 04:08:24 CEST 2012

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? 

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