remd all atom refinement correction on piasek4

Conflicts:

	files/pbs8.csh

diff --git a/files/pbs8.csh b/files/pbs8.csh
index 2f412cc..31d7fb9 100755 (executable)
--- a/files/pbs8.csh
+++ b/files/pbs8.csh
@@ -72,7 +72,7 @@ ln -s file_wham_T*K_ave.pdb ave
 rm ave
 
 #amber min refinement
-foreach x (`seq 1 5`)
+foreach i (`seq 1 5`)
 ../files/refine.sh MODEL$i.pdb
 end
 

diff --git a/files/refine.sh b/files/refine.sh
index 23a022e..88e6b69 100755 (executable)
--- a/files/refine.sh
+++ b/files/refine.sh
@@ -1,30 +1,30 @@
 #!/bin/sh
 # refine.sh plik.pdb
 
-export AMBERHOME=/opt/amber12
-export LD_LIBRARY_PATH=/opt/lib/intel/11.1:/big/appl/lib/
+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
 ln -s $1 tmp1.pdb
-$AMBERHOME/bin/tleap -f /big/appl/amber_refine/leap.bat
+$AMBERHOME/bin/tleap -f /users2/CASP12/EXAMPLES/all-atom/amber_files/leap.bat
 
-/big/appl/mmtsb/perl/convpdb.pl -out generic_noh z_tleap.pdb > noh.pdb
-/opt/pymol-svn/pymol -cq /big/appl/amber_refine/dss.py | awk \
+/users2/local/mmtsb/perl/convpdb.pl -out generic_noh z_tleap.pdb > noh.pdb
+/users2/local/pymol_1.6/pymol -cq /big/appl/amber_refine/dss.py | awk \
 '{ires[NR]=$2;ss[NR]=$3}END{for (i=2;i<=NR;i++) {if (ss[i-1]!=ss[i]&&ss[i-1]=="L") printf "%s;",ires[i];if (ss[i-1]!=ss[i]&&ss[i]=="L") printf "%s;%s\n",ires[i-1],ss[i-1]}}' \
 > zakresy.csv
 
 
-/big/appl/amber_refine/narzuc_RST.pl z_tleap.pdb
+/users2/CASP12/EXAMPLES/all-atom/amber_files/narzuc_RST.pl z_tleap.pdb
 
-/opt/mpich2-1.4.1p1_intel/bin/mpirun \
+/users/software/openmpi-1.8.4/bin/mpirun \
 -machinefile $PBS_NODEFILE -np 4 \
 $AMBERHOME/bin/sander.MPI \
--O -i /big/appl/amber_refine/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_$1.out \
 -c t.crd -ref t.crd
 
 $AMBERHOME/bin/ambpdb -p t.top <restrt> stop.pdb
 
 rm $1
-/big/appl/mmtsb/perl/convpdb.pl -amber -out generic_noh stop.pdb > $1
+/users2/local/mmtsb/perl/convpdb.pl -amber -out generic_noh stop.pdb > $1
 rm tmp1.pdb z_tleap.pdb t.top t.crd leap.log noh.pdb zakresy.csv RST.dat restrt mdinfo stop.pdb