Rafal's code for NMR restraints

[django_unres.git] / files / pbs8_newct-9p.csh

diff --git a/files/pbs8_newct-9p.csh b/files/pbs8_newct-9p.csh
old mode 100755 (executable)
new mode 100644 (file)
index 10d70d5..3e58264
--- a/files/pbs8_newct-9p.csh
+++ b/files/pbs8_newct-9p.csh
@@ -3,15 +3,21 @@
 #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
+#ORG: setenv UNRES_BIN /users2/czarek/UNRES/run/ADAM/unres-mult-symetr_KCC_ifort_MPICH-NEWCORR-SAXS-NMRAMB-Bfac.exe
+#setenv UNRES_BIN /users2/adam/bin/unres-ms_ifort_MPICH_SC-HCD5-DFA-nmr.exe
+#DZIALA: setenv UNRES_BIN /users2/adam/bin/unres-ms_ifort_MPICH_SC-HCD5_nmr.exe
+setenv UNRES_BIN /users2/adam/bin/unres-ms_ifort_MPICH_SC-HCD5_nmr-SAXS.exe
 #-----------------------------------------------------------------------------
-setenv DD /users2/czarek/UNRES/PARAM
+#ORG: setenv DD /users2/czarek/UNRES/PARAM
+setenv DD /users2/adam/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 THETPAR $DD/pot_theta_G631_DIL_ext.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 TORPAR $DD/pot_tor_G631_DIL_ext.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
@@ -20,6 +26,7 @@ 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
+setenv NMRPAR ${DD}/nmr.parm
 #-----------------------------------------------------------------------------
 cd $PBS_O_WORKDIR
 
@@ -35,7 +42,10 @@ setenv OUT1FILE YES
 $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
+#ORG: setenv WHAM_BIN /users2/czarek/UNRES/run/ADAM/wham_ifort_KCC_MPICH-okeanos_NEWCORR-SAXS-NMRAMB-Bfac.exe
+#FAIL: setenv WHAM_BIN /users2/adam/bin/wham_ifort_MPICH-SC-HCD5-nmr-SAXS.exe                                                                                     
+#DZIALA: setenv WHAM_BIN /users2/adam/unres/bin/wham/wham_ifort_MPICH-SC-HCD5-NMR.exe
+setenv WHAM_BIN /users2/adam/bin/wham_ifort_MPICH-SC-HCD5-nmr-SAXS.exe
 setenv CONTFUNC GB
 setenv SIDEP $DD/contact_ext.3.parm
 setenv SCRATCHDIR .
@@ -63,7 +73,8 @@ 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
+#ORG: setenv CLUSTER_WHAM_BIN /users2/czarek/UNRES/run/ADAM/unres_clustMD-mult_ifort_MPICH_NEWCORR-SAXS-MRAMB-bfac.exe
+setenv CLUSTER_WHAM_BIN /users2/adam/bin/unres_clustMD_ifort_MPICH-piasek_SC-HCD5-nmr-SAXS.exe
 
 $MPIRUN -machinefile $PBS_NODEFILE -np 2 $CLUSTER_WHAM_BIN
 
@@ -74,7 +85,7 @@ if `awk '{cap=toupper($0); if (cap!=$0) {print 1;exit}}' file.seq` then
  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)
+ foreach i (`seq 2 2 $numstruc`)
    setenv headval `echo $i "*" $onestruc|bc -l`
    setenv halfi `echo $i/2|bc`
    head -n $headval tmp.pdb | tail -n $onestruc >MODEL${halfi}.pdb
@@ -83,11 +94,12 @@ if `awk '{cap=toupper($0); if (cap!=$0) {print 1;exit}}' file.seq` then
 else
 # proteins with L-aminoacids only
 ln -s file_wham_T*K_ave.pdb ave
+setenv numstruc `awk '/ENERGY/{i++}END{print i/2}' ave`
 ../files/cluster2allatom.sh ave
 rm ave
 
 #amber min refinement
-foreach i (`seq 1 5`)
+foreach i (`seq 1 $numstruc`)
 ../files/refine.sh MODEL$i.pdb $ssbond
 end
 endif
@@ -100,7 +112,7 @@ if ( `grep -c pdbref file.inp` ) then
   grep -v TER plik1ter.pdb | awk '{printf "%s%s%s\n",substr($0,0,21)," ",substr($0,23)}' > tmp.pdb
   /users2/local/mmtsb/perl/convpdb.pl -setchain A -renumber 1 -out generic_noh plik.pdb |grep ATOM > plik1chain.pdb
   /users2/local/mmtsb/perl/convpdb.pl -setchain B -renumber 1 -out generic_noh plik2.pdb |grep ATOM >> plik1chain.pdb  
-  foreach i (`seq 1 5`)
+  foreach i (`seq 1 $numstruc`)
     sed /TER/q MODEL$i.pdb_ > tmp1.pdb
     /users2/local/mmtsb/perl/convpdb.pl -setchain A -renumber 1 -out generic_noh tmp1.pdb |grep ATOM > MODEL${i}chain.pdb    
     sed '0,/TER/d' MODEL$i.pdb_ > tmp2.pdb
@@ -112,11 +124,9 @@ if ( `grep -c pdbref file.inp` ) then
  /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
+ foreach i (`seq 1 $numstruc`)
+ /users2/local/bin/tmscore MODEL${i}.pdb plik1.pdb > tmscore${i}.out
+ end
  if (-e saxs.data) then
   awk -f ../files/saxs_dist.awk plik1.pdb > plik_saxs.data
  endif
@@ -124,13 +134,24 @@ if ( `grep -c pdbref file.inp` ) then
 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
+foreach i (`seq 1 $numstruc`)
+awk -f ../files/saxs_dist.awk MODEL${i}.pdb > MODEL${i}_saxs.data
+end
 ../files/plot_saxs.py
 endif
 
+#NMR:
+if (-e file_wham_T*K_0001.nmr) then
+ setenv LD_LIBRARY_PATH `pwd`/../files/gnuplot:$LD_LIBRARY_PATH
+ foreach i (`seq -f "%04g" 1 $numstruc`)
+ set pl_cur=`ls -1 file_wham_T*K_${i}.nmr`
+ ln -s $pl_cur _a.nmr
+ ../files/gnuplot/gnuplot ../files/nmr_cont.gnu
+ rm _a.nmr
+ mv _a.png `basename $pl_cur nmr`png
+ end
+endif
+
+
 #END
 touch finished