5 #-----------------------------------------------------------------------------
6 setenv UNRES_BIN /users2/czarek/UNRES/run/ADAM/unres-mult-symetr_KCC_ifort_MPICH-NEWCORR-SAXS-NMRAMB-Bfac.exe
7 #-----------------------------------------------------------------------------
8 setenv DD /users2/czarek/UNRES/PARAM
9 setenv BONDPAR $DD/bond_AM1_ext_dum.parm
10 setenv THETPAR $DD/theta_opt.parm.OPT_TRP1_FSD_Villin_E0L_QHK_N9L_LX7_BDD_I18
11 setenv THETPARPDB $DD/thetaml_ext.5parm
12 setenv ROTPARPDB $DD/scgauss_ext.parm
13 setenv ROTPAR $DD/rotamers_AM1_aura_ext.10022007.parm
14 setenv TORPAR $DD/torsion_abinitio.parm-2d-all-DL-03-02-2cos
15 setenv TORDPAR $DD/pot_tord_G631_DIL_ext.parm
16 setenv ELEPAR $DD/electr_631Gdp_ext.parm
17 setenv SIDEPAR $DD/scinter_GB_ext_lip.parm
18 setenv FOURIER $DD/fourier_opt.parm.OPT_TRP1_FSD_Villin_E0L_QHK_N9L_LX7_BDD_I18
19 setenv SCCORPAR $DD/sccor_am1_pawel_ext.dat
20 setenv SCPPAR $DD/scp_ext.parm
21 setenv PATTERN $DD/patterns.cart
22 setenv LIPTRANPAR $DD/Lip_tran_initial_ext.parm
23 #-----------------------------------------------------------------------------
26 setenv MPIRUN "/users2/local/mpich2-1.4.1p1_intel/bin/mpirun "
27 set NPROCS=`cat $PBS_NODEFILE | wc -l`
35 $MPIRUN -machinefile $PBS_NODEFILE -np $NPROCS $UNRES_BIN
38 setenv WHAM_BIN /users2/czarek/UNRES/run/ADAM/wham_ifort_KCC_MPICH-okeanos_NEWCORR-SAXS-NMRAMB-Bfac.exe
40 setenv SIDEP $DD/contact_ext.3.parm
42 setenv PREFIX file_wham
44 $MPIRUN -machinefile $PBS_NODEFILE -np 2 $WHAM_BIN
47 setenv line `awk '{}END{print int(NR*0.2)}' file_GB000.stat`
49 if ( `grep -c pdbref file.inp` ) then
50 tail -q -n +$line file_GB*.stat | awk '{if ( NF == 14 ) print}' >remd_all.stat
51 cat file_GB*.stat | awk '{if ( NF == 14 ) print}' > remd_all0.stat
53 tail -q -n +$line file_GB*.stat | awk '{if ( NF == 10 ) print}' >remd_all.stat
54 cat file_GB*.stat |awk '{if ( NF == 10 ) print}' > remd_all0.stat
56 ../files/matplotlib_hist.py $temperatures
57 rm remd_all.stat remd_all0.stat
60 setenv INPUT file_cluster
61 setenv INTIN file_wham
62 setenv OUTPUT file_cluster
65 setenv PRINTCOOR PRINT_PDB
66 setenv CLUSTER_WHAM_BIN /users2/czarek/UNRES/run/ADAM/unres_clustMD-mult_ifort_MPICH_NEWCORR-SAXS-MRAMB-bfac.exe
68 $MPIRUN -machinefile $PBS_NODEFILE -np 2 $CLUSTER_WHAM_BIN
70 if `awk '{cap=toupper($0); if (cap!=$0) {print 1;exit}}' file.seq` then
71 #no allatom conversion/refinementkx for proteins with D-aminoacids
72 ln -s file_wham_T*K_ave.pdb ave
73 sed -n '/ENERGY/,/ENDMDL/p' ave >tmp.pdb
74 setenv numstruc `grep ENERGY tmp.pdb|wc -l`
75 setenv allline `cat tmp.pdb|wc -l`
76 setenv onestruc `echo $allline "/" $numstruc| bc -l|sed 's/\.0*//'`
77 foreach i (`seq 2 2 $numstruc`)
78 setenv headval `echo $i "*" $onestruc|bc -l`
79 setenv halfi `echo $i/2|bc`
80 head -n $headval tmp.pdb | tail -n $onestruc >MODEL${halfi}.pdb
84 # proteins with L-aminoacids only
85 ln -s file_wham_T*K_ave.pdb ave
86 setenv numstruc `awk '/ENERGY/{i++}END{print i/2}' ave`
87 ../files/cluster2allatom.sh ave
91 foreach i (`seq 1 $numstruc`)
92 ../files/refine.sh MODEL$i.pdb $ssbond
96 /users2/local/pymol_1.6/pymol -c ../files/model.pml
98 if ( `grep -c pdbref file.inp` ) then
99 awk '{printf "%s%s%s\n",substr($0,0,21)," ",substr($0,23)}' plik.pdb > tmp.pdb
100 if ( -f "plik1ter.pdb" ) then
101 grep -v TER plik1ter.pdb | awk '{printf "%s%s%s\n",substr($0,0,21)," ",substr($0,23)}' > tmp.pdb
102 /users2/local/mmtsb/perl/convpdb.pl -setchain A -renumber 1 -out generic_noh plik.pdb |grep ATOM > plik1chain.pdb
103 /users2/local/mmtsb/perl/convpdb.pl -setchain B -renumber 1 -out generic_noh plik2.pdb |grep ATOM >> plik1chain.pdb
104 foreach i (`seq 1 $numstruc`)
105 sed /TER/q MODEL$i.pdb_ > tmp1.pdb
106 /users2/local/mmtsb/perl/convpdb.pl -setchain A -renumber 1 -out generic_noh tmp1.pdb |grep ATOM > MODEL${i}chain.pdb
107 sed '0,/TER/d' MODEL$i.pdb_ > tmp2.pdb
108 /users2/local/mmtsb/perl/convpdb.pl -setchain B -renumber 1 -out generic_noh tmp2.pdb |grep ATOM >> MODEL${i}chain.pdb
109 rm tmp1.pdb tmp2.pdb MODEL$i.pdb_
110 ../files/DockQ.py MODEL${i}chain.pdb plik1chain.pdb > dockq_$i.out
113 /users2/local/mmtsb/perl/convpdb.pl -renumber 1 -out generic tmp.pdb > plik1.pdb
116 foreach i (`seq 1 $numstruc`)
117 /users2/local/bin/tmscore MODEL${i}.pdb plik1.pdb > tmscore${i}.out
119 if (-e saxs.data) then
120 awk -f ../files/saxs_dist.awk plik1.pdb > plik_saxs.data
125 if (-e saxs.data) then
126 foreach i (`seq 1 $numstruc`)
127 awk -f ../files/saxs_dist.awk MODEL${i}.pdb > MODEL${i}_saxs.data
129 ../files/plot_saxs.py