gcif_to_mol2

#!/bin/bash

filename=$1
res=${filename:5:3}

echo "Residue $res"

if [ -f "$res.mol2" ]; then
#  skip modification date check, since Nigel's changes are not key here
#   if [ "$filename" -ot "$res.mol2" ]; then
      echo "    already done: skipping"
      exit 0
#   fi
fi

# Check if PBEh-3c method was used:
egrep '(PBEh-3c|def2-TZVP)' $filename > /dev/null
status=$?
if [ "$status" != 0 ]; then
   echo "    does not use PBEh-3c or def2-TZVP"
   exit 0
fi

# Check for fullerenes
grep fullerene $filename > /dev/null
status=$?
if [ "$status" == 0 ]; then
   echo "    contains fullerene"
   exit 0
fi

# N.B.: right now (Nov. 22) one needs to be on the "geostd" branch for
#   this to work.
$AMBERHOME/bin/antechamber -i $filename -fi ccif -o $res.mol2 -fo mol2  \
    -bk comp_$res -s 0 -dr no \
   -at gaff2 -c abcg2 -ek 'qm_theory="AM1", maxcyc=0, ndiis_attempts=700,'

status=$?
if [ "$status" == 0 ]; then
    $AMBERHOME/bin/parmchk2 -s 2 -i $res.mol2 -f mol2 -o $res.frcmod
fi

/bin/rm -f ANTECH* ATOMTYP* sqm.*