It determines the interaction energy between 2 molecules or 2 groups of molecules. The way it operates is by unfolding the selected targets and determining the stability of the remaining molecules and then subtracting the sum of the individual energies from the global energy. In case there is a metal bound between the two molecules it will assign it to the one which makes the stronger interactions with the metal. The minimal configuration file for AnalyseComplex is:


The user can select which side chain or group of side chains to use to determine the interaction energy with the rest of the protein. The way to do this is by setting the parameter analyseComplexChains:


wherenameMol1nameMol2 (i.e. AB) means that we want to determine the interaction energy of chains Mol1-Mol2 of the pdb molecule against the rest of the molecule. If you don't set it by default the program will calculate all possible interactions between all molecules in the complex. We can also specify which molecules we want to calculate interaction energy against by setting:


where nameMol1,nameMol2 (i.e. A,B or A B or A#B or A\tB) means that we want to determine the interaction energy of chains Mol1 against Mol2.

The option complexwithDNAcan be used with this command, when set to true, automatically will divide the PDB in 2 groups: DNA and Protein and will calculate the interaction between the two.


It can be run using the command line:

FoldX --command=AnalyseComplex --pdb=AC.pdb --analyseComplexChains=A,B --complexWithDNA=true

FoldX uses output-file as a tag to compose labels for the different output files in a batch run.After running BuildModel you'll get four files to look at. Given output-file="TAG" the output files are:

  • Indiv_energies_TAG_AC.fxout -> Independent energies terms for all chains in the pdb
  • Interaction_TAG_AC.fxout -> Energy terms for interaction energy
  • Interface_Residues_TAG_AC.fxout -> Interface residues on the complex (i.e. AC99:A->alanine, C->peptide chain, residue number)
  • Summary_TAG.fxout -> Complex energy summary, contains intraclashes, interaction energy and stability

If you don't set output-file, TAG will be the pdbId of the first pdb on the batch.

The output file contains the standard columns corresponding to the different energy terms (all of them reflecting changes in the respective energies upon binding) plus a column at the beginning showing intrachain clashes of the residues of the selected molecules or group of molecules. This term is important when designing protein complex interfaces since we could have a residue that has a very good interaction with the neighbour chain, but is in a very strained conformation with respect to its own chain. Thus that conformation is not realistic.

The files Indiv_ energies_ and Interaction_ have same headers with the energy terms decomposition in Kcal/mol, the columns are:

Energy terms

Title energy_description
Backbone Clash Backbone-backbone VanderWaals. These are not considered in the total
Backbone Hbond This the contribution of backbone Hbonds
Cis Bond Cost of having a cis peptide bond
Disulfide Contribution of disulfide bonds
Electrostatic Kon Electrostatic interaction between molecules in the precomplex
Electrostatics Electrostatic interactions
Energy Ionisation Contribution of ionisation energy
Entropy Complex Entropy cost of forming a complex
Entropy Main Chain Entropy cost of fixing the main chain
Entropy Side Chain Entropy cost of fixing the side chain
Group1 Chain name of group 1
Group2 Chain name of group 2
Helix Dipole Electrostatic contribution of the helix dipole
Interaction Energy Binding energy
Interface Residues Number of interface residues
Interface Residues BB Clashing Number of interface residues BB clashing
Interface Residues Clashing Number of interface residues that are clashing
Interface Residues VdW Clashing Number of interface residues VdW clashing
IntraclashesGroup1 VanderWaals’ clashes of residues at the interface of the complex with their own molecule
IntraclashesGroup2 VanderWaals’ clashes of residues at the interface of the complex with their own molecule
Partial Covalent Bonds Interactions with bound metals
Pdb Pdb file
Residue Number Number of residues
Sidechain Hbond This the contribution of sidechain-sidechain and sidechain-backbone Hbonds
Solvation Hydrophobic Contribution of hydrophobic groups
Solvation Polar Penalization for burying polar groups
Torsional Clash VanderWaals’ torsional clashes (intraresidue)
Van der Waals Contribution of the VanderWaals
Van der Waals clashes Energy penalization due to VanderWaals’ clashes (interresidue)
Water Bridge Contribution of water bridges