SUMMARY (COMMON FOR ALL SOFTWARES)


  1. First localize the donor and the acceptor residues (residue number)

  2. Preparing the system.
  3. In a simplified view, the electronic coupling is the acceptor/donor molecular orbital overlapping when the electron is transferred. At that point the electron is leaving the donor orbital and is in the pathway of the acceptor, but it doesn't arrive yet. For this reason the system should be prepared with both donor and acceptor in their oxidize form (ox-ox) being involved in the process the LUMOs orbitals (Lowest unoccupied molecular orbitals). If the mechanism of our system is hole transfer we should prepare the system with donor and acceptor in their reduced form (red-red) and we will select the HOMOs (highest occupied molecular orbitals).



  4. Optimize donor and acceptor in their red-red (hole transfer) ox-ox (e-transfer)

  5. Run single point calculation with specific keywords to print the molecular orbitals, the overlap matrix and dipole matrix

  6. Localize the HOMO/LUMO orbitals

  7. Select suitable orbitals to calculate the electronic coupling

  8. Submit the files in e-coupling server