+#PBS -N test_server
+#PBS -q nowy
+#PBS -l nodes=4:ppn=4
+
+#-----------------------------------------------------------------------------
+setenv UNRES_BIN /users2/czarek/UNRES/run/ADAM/unres-mult-symetr_KCC_ifort_MPICH-NEWCORR-SAXS-NMRAMB-Bfac.exe
+#-----------------------------------------------------------------------------
+setenv DD /users2/czarek/UNRES/PARAM
+setenv BONDPAR $DD/bond_AM1_ext_dum.parm
+setenv THETPAR $DD/theta_opt.parm.OPT_TRP1_FSD_Villin_E0L_QHK_N9L_LX7_BDD_I18
+setenv THETPARPDB $DD/thetaml_ext.5parm
+setenv ROTPARPDB $DD/scgauss_ext.parm
+setenv ROTPAR $DD/rotamers_AM1_aura_ext.10022007.parm
+setenv TORPAR $DD/torsion_abinitio.parm-2d-all-DL-03-02-2cos
+setenv TORDPAR $DD/pot_tord_G631_DIL_ext.parm
+setenv ELEPAR $DD/electr_631Gdp_ext.parm
+setenv SIDEPAR $DD/scinter_GB_ext_lip.parm
+setenv FOURIER $DD/fourier_opt.parm.OPT_TRP1_FSD_Villin_E0L_QHK_N9L_LX7_BDD_I18
+setenv SCCORPAR $DD/sccor_am1_pawel_ext.dat
+setenv SCPPAR $DD/scp_ext.parm
+setenv PATTERN $DD/patterns.cart
+setenv LIPTRANPAR $DD/Lip_tran_initial_ext.parm
+#-----------------------------------------------------------------------------
+cd $PBS_O_WORKDIR
+
+setenv MPIRUN "/users2/local/mpich2-1.4.1p1_intel/bin/mpirun "
+set NPROCS=`cat $PBS_NODEFILE | wc -l`
+
+setenv FGPROCS 2
+setenv POT GB
+setenv PREFIX file
+setenv OUT1FILE YES
+
+#UNRES MREMD
+$MPIRUN -machinefile $PBS_NODEFILE -np $NPROCS $UNRES_BIN
+
+#WHAM
+setenv WHAM_BIN /users2/czarek/UNRES/run/ADAM/wham_ifort_KCC_MPICH-okeanos_NEWCORR-SAXS-NMRAMB-Bfac.exe
+setenv CONTFUNC GB
+setenv SIDEP $DD/contact_ext.3.parm
+setenv SCRATCHDIR .
+setenv PREFIX file_wham
+
+$MPIRUN -machinefile $PBS_NODEFILE -np 2 $WHAM_BIN
+
+#test images
+setenv line `awk '{}END{print int(NR*0.2)}' file_GB000.stat`
+
+if ( `grep -c pdbref file.inp` ) then
+ tail -q -n +$line file_GB*.stat | awk '{if ( NF == 14 ) print}' >remd_all.stat
+ cat file_GB*.stat | awk '{if ( NF == 14 ) print}' > remd_all0.stat
+else
+ tail -q -n +$line file_GB*.stat | awk '{if ( NF == 10 ) print}' >remd_all.stat
+ cat file_GB*.stat |awk '{if ( NF == 10 ) print}' > remd_all0.stat
+endif
+../files/matplotlib_hist.py $temperatures
+rm remd_all.stat remd_all0.stat
+
+#CLUSTER WHAM
+setenv INPUT file_cluster
+setenv INTIN file_wham
+setenv OUTPUT file_cluster
+setenv PDB CART
+setenv COORD CX
+setenv PRINTCOOR PRINT_PDB
+setenv CLUSTER_WHAM_BIN /users2/czarek/UNRES/run/ADAM/unres_clustMD-mult_ifort_MPICH_NEWCORR-SAXS-MRAMB-bfac.exe
+
+$MPIRUN -machinefile $PBS_NODEFILE -np 2 $CLUSTER_WHAM_BIN
+
+if `awk '{cap=toupper($0); if (cap!=$0) {print 1;exit}}' file.seq` then
+#no allatom conversion/refinementkx for proteins with D-aminoacids
+ ln -s file_wham_T*K_ave.pdb ave
+ sed -n '/ENERGY/,/ENDMDL/p' ave >tmp.pdb
+ setenv numstruc `grep ENERGY tmp.pdb|wc -l`
+ setenv allline `cat tmp.pdb|wc -l`
+ setenv onestruc `echo $allline "/" $numstruc| bc -l|sed 's/\.0*//'`
+ foreach i (2 4 6 8 10)
+ setenv headval `echo $i "*" $onestruc|bc -l`
+ setenv halfi `echo $i/2|bc`
+ head -n $headval tmp.pdb | tail -n $onestruc >MODEL${halfi}.pdb
+ end
+ rm ave tmp.pdb
+else
+# proteins with L-aminoacids only
+ln -s file_wham_T*K_ave.pdb ave
+../files/cluster2allatom.sh ave
+rm ave
+
+#amber min refinement
+foreach i (`seq 1 5`)
+../files/refine.sh MODEL$i.pdb $ssbond
+end
+endif
+
+/users2/local/pymol_1.6/pymol -c ../files/model.pml
+
+if ( `grep -c pdbref file.inp` ) then
+ awk '{printf "%s%s%s\n",substr($0,0,21)," ",substr($0,23)}' plik.pdb > tmp.pdb
+ /users2/local/mmtsb/perl/convpdb.pl -renumber 1 -out generic tmp.pdb > plik1.pdb
+ rm tmp.pdb
+
+ /users2/local/bin/tmscore MODEL1.pdb plik1.pdb > tmscore1.out
+ /users2/local/bin/tmscore MODEL2.pdb plik1.pdb > tmscore2.out
+ /users2/local/bin/tmscore MODEL3.pdb plik1.pdb > tmscore3.out
+ /users2/local/bin/tmscore MODEL4.pdb plik1.pdb > tmscore4.out
+ /users2/local/bin/tmscore MODEL5.pdb plik1.pdb > tmscore5.out
+ if (-e saxs.data) then
+ awk -f ../files/saxs_dist.awk plik1.pdb > plik_saxs.data
+ endif
+# rm plik1.pdb
+endif
+
+if (-e saxs.data) then
+awk -f ../files/saxs_dist.awk MODEL1.pdb > MODEL1_saxs.data
+awk -f ../files/saxs_dist.awk MODEL2.pdb > MODEL2_saxs.data
+awk -f ../files/saxs_dist.awk MODEL3.pdb > MODEL3_saxs.data
+awk -f ../files/saxs_dist.awk MODEL4.pdb > MODEL4_saxs.data
+awk -f ../files/saxs_dist.awk MODEL5.pdb > MODEL5_saxs.data
+../files/plot_saxs.py
+endif
+
+#END
+touch finished