From 78e8cb3f098dd1ac48d7036c1a27457dfee55663 Mon Sep 17 00:00:00 2001
From: Cezary Czaplewski <czarek@chem.univ.gda.pl>
Date: Thu, 24 Aug 2017 18:49:46 +0200
Subject: [PATCH] remd - amber all atom min refinement

Conflicts:

	files/pbs8.csh
---
 django_simple/todo/templates/details.html |   10 +++++-----
 files/pbs8.csh                            |    6 ++++++
 files/refine.sh                           |   30 +++++++++++++++++++++++++++++
 3 files changed, 41 insertions(+), 5 deletions(-)
 create mode 100755 files/refine.sh

diff --git a/django_simple/todo/templates/details.html b/django_simple/todo/templates/details.html
index f8c9c53..f9651c0 100644
--- a/django_simple/todo/templates/details.html
+++ b/django_simple/todo/templates/details.html
@@ -357,7 +357,7 @@ Created {{ task.created_date  }}
 
 			<li class="list-group-item task-item">
 			  <div class="col-xs-10"> model1 after conversion
-			  to allatom with PULCHRA and SCWRL
+			  to allatom 
 			  {{ task.remd_model1|linebreaks }}
 			  </div>
 			  <div class="col-xs-10"> 
@@ -369,7 +369,7 @@ Created {{ task.created_date  }}
 			</li>
 			<li class="list-group-item task-item">
 			  <div class="col-xs-10"> model2 after conversion
-			  to allatom with PULCHRA and SCWRL
+			  to allatom 
 			  {{ task.remd_model2|linebreaks }}
 			  </div>
 			  <div class="col-xs-10"> 
@@ -381,7 +381,7 @@ Created {{ task.created_date  }}
 			</li>
 			<li class="list-group-item task-item">
 			  <div class="col-xs-10"> model3 after conversion
-			  to allatom with PULCHRA and SCWRL
+			  to allatom 
 			  {{ task.remd_model3|linebreaks }}
 			  </div>
 			  <div class="col-xs-10"> 
@@ -393,7 +393,7 @@ Created {{ task.created_date  }}
 			</li>
 			<li class="list-group-item task-item">
 			  <div class="col-xs-10"> model4 after conversion
-			  to allatom with PULCHRA and SCWRL
+			  to allatom 
 			  {{ task.remd_model4|linebreaks }}
 			  </div>
 			  <div class="col-xs-10"> 
@@ -405,7 +405,7 @@ Created {{ task.created_date  }}
 			</li>
 			<li class="list-group-item task-item">
 			  <div class="col-xs-10"> model5 after conversion
-			  to allatom with PULCHRA and SCWRL
+			  to allatom 
 			  {{ task.remd_model5|linebreaks }}
 			  </div>
 			  <div class="col-xs-10"> 
diff --git a/files/pbs8.csh b/files/pbs8.csh
index d7ec507..2f412cc 100755
--- a/files/pbs8.csh
+++ b/files/pbs8.csh
@@ -70,6 +70,12 @@ $MPIRUN -machinefile $PBS_NODEFILE -np 2 $CLUSTER_WHAM_BIN
 ln -s file_wham_T*K_ave.pdb ave
 ../files/cluster2allatom.sh ave
 rm ave
+
+#amber min refinement
+foreach x (`seq 1 5`)
+../files/refine.sh MODEL$i.pdb
+end
+
 /users2/local/pymol_1.6/pymol -c ../files/model.pml
 
 /users2/local/bin/tmscore MODEL1.pdb plik.pdb > tmscore1.out
diff --git a/files/refine.sh b/files/refine.sh
new file mode 100755
index 0000000..23a022e
--- /dev/null
+++ b/files/refine.sh
@@ -0,0 +1,30 @@
+#!/bin/sh
+# refine.sh plik.pdb
+
+export AMBERHOME=/opt/amber12
+export LD_LIBRARY_PATH=/opt/lib/intel/11.1:/big/appl/lib/
+
+rm -f tmp1.pdb
+ln -s $1 tmp1.pdb
+$AMBERHOME/bin/tleap -f /big/appl/amber_refine/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 \
+'{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
+
+/opt/mpich2-1.4.1p1_intel/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_$1.out \
+-c t.crd -ref t.crd
+
+$AMBERHOME/bin/ambpdb -p t.top <restrt> stop.pdb
+
+rm $1
+/big/appl/mmtsb/perl/convpdb.pl -amber -out generic_noh stop.pdb > $1
+rm tmp1.pdb z_tleap.pdb t.top t.crd leap.log noh.pdb zakresy.csv RST.dat restrt mdinfo stop.pdb
+
-- 
1.7.9.5