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.
- Before saving the parameters or generating the XML file, go to Settings / Tools -> Settings and Enable expert mode
- Go into the POEM++ preprocessor and enter Expert Settings -> End Output and add InteractionEnergyEval to the list.
- generate a normal PFF02 constant temperature run as shown in POEM++ - First Steps
- automate the generation of these jobs as shown in Automated Generation of Jobs
- 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.