Included comment
#!/bin/sh
-# Check for gmx
-#GMX=$(which gmx)
-#if [ ! -n "${GMX}"]; then
-# echo "Gromacs not found! Make sure your Gromacs installation is in your path."
-# exit 1
-#fi
-#GROMACS_DIR=$(basename ${GMX} /bin/gmx)
-#cp ${GROMACS_DIR}/share/gromacs/top/amber03.ff/tip3p.itp tip3p_jc2008.ff/
+# Make the forcefield and symlink it here.
+cd ../../gromacs_config || exit 1
+bash makeff.sh
+cd ../prep/1_pdb2gmx || exit 1
ln -s ../../gromacs_config/tip3p_ionsjc2008.ff tip3p_ionsjc2008.ff
gmx pdb2gmx \
