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 tmp1
   8 ln -s $1 tmp1.pdb
   9
  10 cat << EOF >leap.bat
  11 source leaprc.ff14SB
  12 xx3 = loadpdb tmp1.pdb
  13 EOF
  14
  15 pdb=$1
  16 shift
  17 while true; do
  18         if [ $1 ]; then
  19                 echo bond xx3.$1.SG xx3.$2.SG >> leap.bat
  20                 awk -v ires=$1 -f ../files/cyx.awk $pdb > tmp1
  21                 awk -v ires=$2 -f ../files/cyx.awk tmp1 > $pdb
  22                 shift
  23                 shift
  24         else
  25                 break
  26         fi
  27 done
  28 cat << EOF >> leap.bat
  29 saveamberparm xx3 t.top t.crd
  30 savepdb xx3 z_tleap.pdb
  31 quit
  32 EOF
  33
  34 $AMBERHOME/bin/tleap -f leap.bat
  35
  36 /users2/local/mmtsb/perl/convpdb.pl -out generic_noh z_tleap.pdb > noh.pdb
  37 /users2/local/pymol_1.6/pymol -cq /users2/CASP12/EXAMPLES/all-atom/amber_files/dss.py | awk \
  38 '{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;%s\n",ires[i-1],ss[i-1];if (ss[i-1]!=ss[i]&&ss[i]!="L") printf "%s;",ires[i];}}' \
  39 > zakresy.csv
  40
  41
  42 /users2/CASP12/EXAMPLES/all-atom/amber_files/narzuc_RST.pl z_tleap.pdb
  43
  44 /users/software/openmpi-1.8.4/bin/mpirun \
  45 -machinefile $PBS_NODEFILE -np 4 \
  46 $AMBERHOME/bin/sander.MPI \
  47 -O -i /users2/CASP12/EXAMPLES/all-atom/amber_files/min1.in -p t.top -o amber_min_$pdb.out \
  48 -c t.crd -ref t.crd
  49
  50 $AMBERHOME/bin/ambpdb -p t.top <restrt> stop.pdb
  51
  52 rm $pdb
  53 cp stop.pdb ${pdb}_
  54 /users2/local/mmtsb/perl/convpdb.pl -amber -out generic_noh stop.pdb > $pdb
  55 rm tmp1.pdb z_tleap.pdb t.top t.crd leap.log noh.pdb zakresy.csv RST.dat restrt mdinfo stop.pdb
  56