Energy decomposition analysis (EDA) is a quantitative means of understanding chemical bonds. The way that we go about EDA provides information about the Coulomb and van der Waals energies for different residues of interest.

We go about performing EDA using a Fortran90 program adapted by Dr. Cisneros. The program uses an input file (described here) that includes some specific information about the system being studied, including the number of residues in the associated mdcrd file. One thing to note for the Fortran90 program is that the input files must be in ASCII format. Starting with AMBER16, the default format for all generated files is NetCDF and not ASCII; unless you explicitly set ioutfm=0 in your mdin files, you will have them in NetCDF format. To check if your mdcrd is in ASCII format, use something like head _____.mdcrd. If you see neat rows of numbers, then it is in ASCII. If it looks like your computer is exploding in the Terminal, then you’ll need to use cpptraj to create an ASCII formatted mdcrd. Another (easier) way to do this is to use file _____.mdcrd. If the file is a NetCDF, then _____.mdcrd: data would be returned; otherwise _____.mdcrd: ASCII text will be returned. You can use cpptraj to convert to ASCII through adding

trajout _____.mdcrd crd

to the end of your a cpptraj input (that includes all the trajin lines for files of interest). It is critically important that any time cpptraj is used to convert to ASCII format that no strip commands are used. Stripping the system, while saving on time, will return radically different values for both Coulomb and van der Waals energies. Using autoimage will have an effect on the significant figures, so it should also not be used.

Once the Fortran90 program has run (correctly), there are 3 output files generated. These are fort.804, fort.803, and fort.806. The first one, fort.804, is a sanity check that may include the atom typing. It is created at the start of the program execution. The other two files, fort.803 and fort.806, are created after the program has finished. fort.803 includes information about the Coulomb energies; fort.806 includes information about the van der Waals energies. For both of these files, the columns are organized from left to right as:

  1. Index (row number)
  2. Residue A
  3. Residue B
  4. Coulomb or van der Waals energy (in kcal mol-1)
  5. Standard error