- Create a topology file for CHARMM, atom ordering is important.
- Calculate the ESP using Gaussian, taking care to preserve ordering.
- Fit an MDCM model, generation of the frames.txt file should also preserve ordering.
- For fMDCM, an atom-charge-dictionary linking the charges to their parent atom is required. This must also preserve ordering.
$BINDIR/comb-xyz-to-dcm.pl $XYZFILE $DCUBE