semi_empirical_parameterization.info

## The following example shows how to obtained forcefield parameter of Benzene with charges obtained using semi-empirical method "AM1" and bonded and non-bonded parameters from GAFF2 forcefield
You will need the following command line tools:
  1. Obabel for convert "SMILES" to PDBs
  2. pbd4amber from AmberTools to convert the PDB into GAFF2 compitable PDB
  3. Antechamber to fit AM1 charges and convert the PDB file to mol2 file
  4. parmchk2 for obtained .frcmod file

Step #1: Use the following obabel command to convert benzene SMILEs to PBD
  '''
  obabel -:"c1ccccc1" -O benzene.pdb
  '''
Step #2: Use the following pbd4amber command to conver the benzene.pdb file to GAFF2 compitable file
  '''
  pdb4amber -i benzene.pdb -o benzene_amber.pdb
  '''
Step #3: Now use Antechamber to conver the processed pdb file to a mol2 file with charges obatained using the semi-empirical quantum mechanics methods "AM1"
  '''
  antechamber -i benzene_amber.pdb -fi pdb -o benzene_amber.mol2 -fo mol2 -c bcc -s 2 -at gaff -nc 0 -pl 10
  '''
Wait till the process finishes
Step #4: Use Parmchk2 to obtaine the .frcmod file
  '''
  parmchk2 -i benzene_amber.mol2 -f mol2 -o benzene_amber.frcmod -s gaff2
  '''

That's all, make sure to read the .frcmod file for any "WARNING", "ATTENTION" or "MISSING" parameters.