To run e-coupling calculations, click in the buttons to submit the input files, choose the method, the type of orbitals and specify the number of the residues involved in the reaction and the number of atoms selected. You should also specify the minimum tolerance: minimum population accepted to consider one orbital place on one residue
ECServer generates a log file and four different graphical representations of the results. The logfile has different parts:
*** E-COUPLING INPUT SUMMARY ***
The first block enumerates the parameters from the input file, including name of the files, number and type of orbitals chosen, the approximation used (FCD, GMH), the number of atoms belonging the donor, acceptor and bridge and the minimum charge tolerance. The tolerance is the minimum value that we will accept to consider one orbital placed in donor or acceptor residues. For example, tolerance 0.9 means that only orbitals with population higher that 90% will be consider in a residue.
***E-COUPLING MOLECULAR ORBITAL INFORMATION***
We can find in this part some information extracted from the QM input, as the number of atoms, energy of each molecular orbital (Hartee), and its localization (the percentage of donor/acceptor/bridge) etc.
We can read the contribution from donor and acceptor in each orbital. For example HOMO (orbital number 111) is 98% placed in the donor (occupancy=0.98) whereas the 2% is placed on the bridge.
**Note: If all the values in %DonorCharge or %AcceptorCharge column are 0 , check the residue or atom selection. If the option 'bridge' is no selected , the %BridgeCharge values are 0.
*** RESULTS E-COUPLING CALCULATIONS WITH FCD METHOD (TWO-STATES)***
Electronic coupling calculations were printed by pairs from donor and acceptor orbitals.
After the results per pairs, the rmsVDA value is printed.
RESULTS. GRAPHICAL REPRESENTATION
Graphical representation includes: donor/acceptor orbital energies(A), EC values per orbital pairs with proportional circles (B) and bars (C) and energy difference per orbital pairs(D).