+#PBS -N test_server
+#PBS -q nowy
+#PBS -l nodes=4:ppn=4
+
+#-----------------------------------------------------------------------------
+setenv UNRES_BIN /users2/czarek/UNRES/git3_tmp/build/bin/unresMD-mult_ifort_MPI_E0LL2Y.exe
+#-----------------------------------------------------------------------------
+setenv DD /users2/czarek/UNRES/git3_tmp/unres/PARAM
+setenv BONDPAR $DD/bond_AM1_ext_dum.parm
+setenv THETPAR $DD/theta_abinitio-ext-old.parm
+setenv THETPARPDB $DD/thetaml_ext.5parm
+setenv ROTPARPDB $DD/scgauss_ext.parm
+setenv ROTPAR $DD/rotamers_AM1_aura_ext.10022007.parm
+setenv TORPAR $DD/tor_opt_iter1_7p_old-ext.parm
+setenv TORDPAR $DD/pot_tord_G631_DIL_ext.parm
+setenv ELEPAR $DD/electr_631Gdp_ext.parm
+setenv SIDEPAR $DD/sc_GB_opt_iter1_7p_old-ext_lip.parm
+setenv FOURIER $DD/fourier_opt_iter1_7p_old-ext.parm
+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/git3_tmp/build/bin/wham-mult_ifort_MPI_E0LL2Y.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 $temperatures
+rm remd_all.stat remd_all0.stat
+
+#CLUSTER WHAM
+setenv INPUT file_cluster
+setenv INTIN file_wham
+setenv OUTPUT file_cluster
+setenv PDB CART
+setenv COORD CX
+setenv PRINTCOOR PRINT_PDB
+setenv CLUSTER_WHAM_BIN /users2/czarek/UNRES/git3_tmp/build/bin/cluster_wham-mult_ifort_MPI_E0LL2Y.exe
+
+$MPIRUN -machinefile $PBS_NODEFILE -np 2 $CLUSTER_WHAM_BIN
+
+ln -s file_wham_T*K_ave.pdb ave
+../files/cluster2allatom.sh ave
+rm ave
+
+#amber min refinement
+foreach i (`seq 1 5`)
+../files/refine.sh MODEL$i.pdb
+end
+
+/users2/local/pymol_1.6/pymol -c ../files/model.pml
+
+/users2/local/bin/tmscore MODEL1.pdb plik.pdb > tmscore1.out
+/users2/local/bin/tmscore MODEL2.pdb plik.pdb > tmscore2.out
+/users2/local/bin/tmscore MODEL3.pdb plik.pdb > tmscore3.out
+/users2/local/bin/tmscore MODEL4.pdb plik.pdb > tmscore4.out
+/users2/local/bin/tmscore MODEL5.pdb plik.pdb > tmscore5.out
+
+#END
+touch finished