4 export AMBERHOME=/users2/local/amber/amber14
5 export LD_LIBRARY_PATH=/users2/local/lib/intel/composer_xe_2015/intel64:${LD_LIBRARY_PATH}
12 xx3 = loadpdb tmp1.pdb
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
28 cat << EOF >> leap.bat
29 saveamberparm xx3 t.top t.crd
30 savepdb xx3 z_tleap.pdb
34 $AMBERHOME/bin/tleap -f leap.bat
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];}}' \
42 /users2/CASP12/EXAMPLES/all-atom/amber_files/narzuc_RST.pl z_tleap.pdb
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 \
50 $AMBERHOME/bin/ambpdb -p t.top <restrt> stop.pdb
53 /users2/local/mmtsb/perl/convpdb.pl -amber -out generic_noh stop.pdb > $pdb
54 rm tmp1.pdb z_tleap.pdb t.top t.crd leap.log noh.pdb zakresy.csv RST.dat restrt mdinfo stop.pdb