Initially you must add hydrogens to all atoms in the ligand, ensuring their valences are completed. This can be done using a molecular modeling package. Make sure that the atom types are correct before adding hydrogens. You may want to specify the pH, depending on whether charged or neutral carboxylates and amides are desired.
Next, assign partial atomic charges to the molecule. AMPAC or MOPAC can be used to generate partial atomic charges for the ligand. These charges must be written out in PDBQ format, which has the same columns as a Brookhaven PDB format, but with an added column of partial atomic charges (see `
cartopdbq
' and `
mol2topdbq
' in Appendix
See Shell Scripts and Awk Programs
).