Usage information

avoDna2gmx.sh

-# pdb_mod.sh --find-atom "HTER" -i ATGCTACG_AVO.pdb
-# pdb_mod.sh --find-atom "OXT" -i ATGCTACG_AVO.pdb
-# pdb_mod.sh --replace "HTER" "H5T" -i ATGCTACG_AVO.pdb --filter DA -o ATGCTACG_MOD.pdb -x
-# pdb_mod.sh --replace "OXT" "O5'" -i ATGCTACG_MOD.pdb --filter DA -f -o ATGCTACG_MOD.pdb -x
-
 source $MWSHPATH/out.sh
 
 EXPERT=0
 
 while test $# -gt 0; do
   case "$1" in
+    -u|--usage|-h|--help)
+      echo -e $colBold"Usage for "$colFunc"avoDna2gmx.sh"$colClear":"
+      echo
+      echo -e "This script will attempt to modify a PDB containing DNA chains produced"
+      echo -e "by Avogadro's DNA builder so that it plays ball with GROMACS' pdb2gmx,"
+      echo -e "and matches the atom naming schemes in the CHARMM36 force fields."
+      echo 
+      echo -e $colFunc"avoDna2gmx.sh"$colClear$colArg" --input <PDB> [--output <PDB>] [-expert]"$colClear
+      echo 
+      echo -e $colArg"-i|--input"$colClear" Specify input"$colClear
+      echo -e $colArg"-o|--output"$colClear" Specify output"$colClear
+      echo -e $colArg"-x|--expert"$colClear" Hide warnings"$colClear
+      exit
+      ;;
     -i|--input)
       shift
       INPUT=$1