First version of Avogadro DNA PDB converted for pdb2gmx compatibility

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
+    -i|--input)
+      shift
+      INPUT=$1
+      shift
+      ;;
+    -o|--output)
+      shift
+      OUTPUT=$1
+      shift
+      ;;
+    -x|--expert)
+      shift
+      EXPERT=1
+      ;;
+    *)
+      warningOut "Unrecognised CLI flag: $colArg$1"
+      break
+      ;;
+  esac
+done
+
+if [[ -z $INPUT ]] ; then 
+  errorOut "No input file specified."
+  exit
+fi
+if [[ -z $OUTPUT ]] ; then 
+  OUTPUT=$(echo "$INPUT" | sed 's/AVO/MOD/' | sed 's/avo/mod/')
+  if [ $EXPERT -eq 0 ] ; then
+    warningOut "No output file specified. Defaulted to $colFile""$OUTPUT"
+  fi
+fi
+if [[ $INPUT == $OUTPUT ]] ; then 
+  if [ $FORCE -eq 1 ] ; then
+    if [ $EXPERT -eq 0 ] ; then
+      warningOut "Overwriting $colFile"$INPUT"$colWarning!"
+    fi
+  else
+    errorOut "Overwriting is not permitted. Select different input and output files. (ignore with -f)"
+    exit
+  fi
+fi
+
+if [[ -z $INPUT ]] ; then 
+  errorOut "No input file specified."
+  exit
+fi
+
+if [[ "$OUTPUT" == "__temp__" ]] ; then 
+  errorOut "Choose a different output name."
+  exit
+fi
+
+# PDB Summary
+pdb_mod.sh --summary $INPUT
+pdb_mod.sh --summary $INPUT --filter A -rlo # Chain A
+pdb_mod.sh --summary $INPUT --filter B -rlo # Chain B
+echo ""
+
+N3TER=0
+N5TER=0
+TER_NUM=0
+
+# Deal with termini
+headerOut "Renaming termini atoms:"
+pdb_mod.sh --replace "HTER" "H5T" -i $INPUT -o $OUTPUT -x
+RET=$?
+let "N5TER = N5TER + RET"
+pdb_mod.sh --replace "OXT" "O5'" -i $OUTPUT -f -o $OUTPUT -x
+pdb_mod.sh --replace "HCAP" "H3T" -i $OUTPUT -f -o $OUTPUT -x
+RET=$?
+let "N3TER = N3TER + RET"
+let "TER_NUM = N5TER + N3TER"
+echo ""
+
+if [ $TER_NUM -ne 0 ] ; then
+  headerOut "You will likely have to select $TER_NUM termini when using $colFunc""pdb2gmx"
+  headerOut "$N5TER x $colArg""5TER"
+  headerOut "$N3TER x $colArg""3TER"
+  echo ""
+fi
+
+# Deal with backbone
+headerOut "Renaming backbone atoms:"
+pdb_mod.sh --replace "H5'1" "H5'" -i $OUTPUT -f -o $OUTPUT -x
+pdb_mod.sh --replace "H5'2" "H5''" -i $OUTPUT -f -o $OUTPUT -x
+pdb_mod.sh --replace "H2'1" "H2'" -i $OUTPUT -f -o $OUTPUT -x
+pdb_mod.sh --replace "H2'2" "H2''" -i $OUTPUT -f -o $OUTPUT -x
+
+echo ""
+
+headerOut "Now try to run pdb2gmx:"
+echo -e "$colFunc""source"$colClear" $colFile\$GROMAX/load_gmx.sh"$colClear
+echo -e "$colFunc""source"$colClear" $colFile\$GROMAX/gmx_funcs.sh"$colClear
+echo -e "$colFunc""gromax$colClear "$colFunc"pdb2gmx$colClear $colArg-inter -f $colFile$OUTPUT$colArg"
+
+echo ""