pbs = '#PBS -l nodes='+str(nodes)+':ppn=4'
else:
pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
+
+ tmp_ss=''
+ ix=0
+ if seq[0]=='X':
+ ix=1
+ if instance.ssbond!='':
+ l=[]
+ ss=json.loads(instance.ssbond)
+ for e in ss:
+ l.append(e[0]-ix)
+ l.append(e[1]-ix)
+ tmp_ss=' '.join(map(str,l))
os.chdir(instance.jobdirname)
if instance.unres_ff =='E0LL2Y':
for line in f1:
if '#PBS -l nodes=4:ppn=4' in line:
f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs))
+ elif '$ssbond' in line:
+ f2.write(line.replace('$ssbond',tmp_ss))
else:
tmp1=json.loads(instance.remd_multi_t)
f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
--- /dev/null
+{
+if (int(substr($0,24,3))==ires)
+ print gensub(/CYS/,"CYX","g")
+else
+ print $0
+}
\ No newline at end of file
#amber min refinement
foreach i (`seq 1 5`)
-../files/refine.sh MODEL$i.pdb
+../files/refine.sh MODEL$i.pdb $ssbond
end
/users2/local/pymol_1.6/pymol -c ../files/model.pml
#amber min refinement
foreach i (`seq 1 5`)
-../files/refine.sh MODEL$i.pdb
+../files/refine.sh MODEL$i.pdb $ssbond
end
/users2/local/pymol_1.6/pymol -c ../files/model.pml
export AMBERHOME=/users2/local/amber/amber14
export LD_LIBRARY_PATH=/users2/local/lib/intel/composer_xe_2015/intel64:${LD_LIBRARY_PATH}
-rm -f tmp1.pdb
+rm -f tmp1.pdb tmp1
ln -s $1 tmp1.pdb
-$AMBERHOME/bin/tleap -f /users2/CASP12/EXAMPLES/all-atom/amber_files/leap.bat
+
+cat << EOF >leap.bat
+source leaprc.ff14SB
+xx3 = loadpdb tmp1.pdb
+EOF
+
+pdb=$1
+shift
+while true; do
+ if [ $1 ]; then
+ echo bond xx3.$1.SG xx3.$2.SG >> leap.bat
+ awk -v ires=$1 -f ../files/cyx.awk $pdb > tmp1
+ awk -v ires=$2 -f ../files/cyx.awk tmp1 > $pdb
+ shift
+ shift
+ else
+ break
+ fi
+done
+cat << EOF >> leap.bat
+saveamberparm xx3 t.top t.crd
+savepdb xx3 z_tleap.pdb
+quit
+EOF
+
+$AMBERHOME/bin/tleap -f leap.bat
/users2/local/mmtsb/perl/convpdb.pl -out generic_noh z_tleap.pdb > noh.pdb
/users2/local/pymol_1.6/pymol -cq /users2/CASP12/EXAMPLES/all-atom/amber_refine/dss.py | awk \
/users/software/openmpi-1.8.4/bin/mpirun \
-machinefile $PBS_NODEFILE -np 4 \
$AMBERHOME/bin/sander.MPI \
--O -i /users2/CASP12/EXAMPLES/all-atom/amber_files/min1.in -p t.top -o amber_min_$1.out \
+-O -i /users2/CASP12/EXAMPLES/all-atom/amber_files/min1.in -p t.top -o amber_min_$pdb.out \
-c t.crd -ref t.crd
$AMBERHOME/bin/ambpdb -p t.top <restrt> stop.pdb
-rm $1
-/users2/local/mmtsb/perl/convpdb.pl -amber -out generic_noh stop.pdb > $1
+rm $pdb
+/users2/local/mmtsb/perl/convpdb.pl -amber -out generic_noh stop.pdb > $pdb
rm tmp1.pdb z_tleap.pdb t.top t.crd leap.log noh.pdb zakresy.csv RST.dat restrt mdinfo stop.pdb