SIMONAPreprocessor
Calculation of Interaction Energy of Protein Complexes

To calculate the Interaction Energy of Protein Complexes, as in Meliciani et al.

“Probing Hot Spots on Protein-protein Interfaces with All-atom Free-energy Simulation.” The Journal of Chemical Physics 131, no. 3 (July 21, 2009): 034114–11.

  1. Before saving the parameters or generating the XML file, go to Settings / Tools -> Settings and Enable expert mode
  2. Go into the POEM++ preprocessor and enter Expert Settings -> End Output and add InteractionEnergyEval to the list.
  3. generate a normal PFF02 constant temperature run as shown in POEM++ - First Steps
  4. automate the generation of these jobs as shown in Automated Generation of Jobs
  5. When running the jobs, POEM will show the interaction energy at the end. This is done by offsetting the proteins binding partners by 1000 Angstroem each.