antechamber_script

#!/bin/bash -v

#echo "Starting openbabel to add H atoms to the ligand" 
# Use Babel to add H atoms [ this is already done on converting SDF files to PDB]
#babel -h -ipdb $ligand.pdb -opdb $ligand.babel-h.pdb >> $molname.err 
#obabel -h -ipdb $ligand.pdb -opdb $ligand.babel-h.pdb >> $molname.err

#if [ ! -s $ligand.babel-h.pdb ]
#then
#        echo "FAILURE: Unable to add H atoms to the ligand. Some likely reasons are invalid pdb format or very non-standard atom name. Check to make sure atom name starts in column 14 of the pdb file. Check the $molname.err file for clues."
#     exit 1
#else

# Prepare/read in ligand parameters

# Set initial ligand net charge to zero or whatever is appropriate [filled in by parameterize-it]
   #ligand_charge=0

   echo "Starting antechamber to create prep file for tleap. Assuming ligand net charge = "  $ligand_charge >> $molname.err
# Use Amber Antechamber to create tleap prepi file
   $ACHOME/bin/antechamber -nc $ligand_charge -s 2 -c bcc -i $ligand.pdb -fi pdb -o pdb2pqr.ligand.prepi -fo prepi -at gaff >> $molname.err 
   if [ ! -s pdb2pqr.ligand.prepi ]
   then
      echo "WARNING: Likely inconsistency between the assumed net charge and the number of electrons."
   fi
#fi