files/refine.sh

   1 #!/bin/sh
   2 # refine.sh plik.pdb
   3
   4 export AMBERHOME=/users2/local/amber/amber14
   5 export LD_LIBRARY_PATH=/users2/local/lib/intel/composer_xe_2015/intel64:${LD_LIBRARY_PATH}
   6
   7 rm -f tmp1.pdb
   8 ln -s $1 tmp1.pdb
   9 $AMBERHOME/bin/tleap -f /users2/CASP12/EXAMPLES/all-atom/amber_files/leap.bat
  10
  11 /users2/local/mmtsb/perl/convpdb.pl -out generic_noh z_tleap.pdb > noh.pdb
  12 /users2/local/pymol_1.6/pymol -cq /big/appl/amber_refine/dss.py | awk \
  13 '{ires[NR]=$2;ss[NR]=$3}END{for (i=2;i<=NR;i++) {if (ss[i-1]!=ss[i]&&ss[i-1]=="L") printf "%s;",ires[i];if (ss[i-1]!=ss[i]&&ss[i]=="L") printf "%s;%s\n",ires[i-1],ss[i-1]}}' \
  14 > zakresy.csv
  15
  16
  17 /users2/CASP12/EXAMPLES/all-atom/amber_files/narzuc_RST.pl z_tleap.pdb
  18
  19 /users/software/openmpi-1.8.4/bin/mpirun \
  20 -machinefile $PBS_NODEFILE -np 4 \
  21 $AMBERHOME/bin/sander.MPI \
  22 -O -i /users2/CASP12/EXAMPLES/all-atom/amber_files/min1.in -p t.top -o amber_min_$1.out \
  23 -c t.crd -ref t.crd
  24
  25 $AMBERHOME/bin/ambpdb -p t.top <restrt> stop.pdb
  26
  27 rm $1
  28 /users2/local/mmtsb/perl/convpdb.pl -amber -out generic_noh stop.pdb > $1
  29 rm tmp1.pdb z_tleap.pdb t.top t.crd leap.log noh.pdb zakresy.csv RST.dat restrt mdinfo stop.pdb
  30