--- /dev/null
+#!/bin/csh -f
+
+# Provide names of the pdb files
+set protein1 = 1UDI_A.pdb
+set protein2 = 1UDI_B.pdb
+
+# Provide number of steps in milions
+set nstep = 0.05
+
+# Provide number of clusters
+set nclust = 10
+
+# Provide temperature of clustering
+set temper = 300
+
+# Provide UNRES instalation pathway
+set UNRES = /users2/vetinari/unres_hom_m/unres
+
+
+
+################################################################################
+################################################################################
+################################################################################
+sed -e "s=UUU=$UNRES=" start_unres_example.mat > start_unres.mat
+sed -e "s=UUU=$UNRES=" start_wham_example.mat > start_wham.mat
+sed -e "s=UUU=$UNRES=" start_cluster_example.mat > start_cluster.mat
+
+
+# Generation of initial orientations
+echo "Generation of initial orientations"
+echo "TER" > TER
+#gfortran -O3 generator_v13b.f -o generator_v13b
+#./generator_v13b $protein1 $protein2 0 > log
+grep -v "TER" $protein1 > prot1
+grep -v "TER" $protein2 > prot2
+cat prot1 "TER" prot2 > reference.pdb
+rm TER prot1 prot2
+
+
+################################################################################
+# Setting up and running MREMD
+echo "Setting up and running MREMD"
+set nstep2 = `echo $nstep \* 1000000 | bc | awk -F "." '{print $1}'`
+set box = `grep -A1 "Boxsize (suggested)" log | tail -1 | cut -c 3-8`
+sed "s/boxxx/$box/g" unres_example.inp > unres_dock.inp
+sed "s/NNN/$nstep2/g" unres_dock.inp > unres_dock.in
+mv unres_dock.in unres_dock.inp
+
+#qsub start_unres.mat
+
+
+
+################################################################################
+# Setting up and running WHAM analysis
+echo "Setting up and running WHAM analysis"
+#set resnum = `grep -A 1 "PDB data will be read from file" dimer.out_GB000 | tail -1 | awk '{print $2}'`
+#set resnum = `echo $resnum + 5 | bc`
+
+#grep -A $resnum "PDB data will be read from file" dimer.out_GB000 | grep -B 9999 "nsup=" | egrep -v "PDB|Nres:|nsup=" | awk '{print $3}' > seq_raw
+
+egrep "CA|TER" reference.pdb > temp.pdb
+set res1 = `grep -B 9999 "TER" temp.pdb | grep -v TER | grep -c CA`
+set res2 = `grep -A 9999 "TER" temp.pdb | grep -v TER | grep -c CA`
+set start1 = `head -1 temp.pdb | awk '{print $4}'`
+set end2 = `tail -1 temp.pdb | awk '{print $4}'`
+set start2 = `grep -A 1 TER temp.pdb | tail -1 | awk '{print $4}'`
+set end1 = `grep -B 1 TER temp.pdb | head -1 | awk '{print $4}'`
+
+echo First protein has $res1 residues, while second molecule has $res2 residues.
+echo $start1 $end1 $start2 $end2
+
+rm seq_raw
+
+if ($start1 != GLY) then
+echo D > seq_raw
+endif
+
+head -$res1 temp.pdb | awk '{print $4}' >> seq_raw
+
+if ($end1 != GLY) then
+echo D >> seq_raw
+endif
+
+if ($start2 != GLY) then
+echo D >> seq_raw
+endif
+
+tail -$res2 temp.pdb | awk '{print $4}' >> seq_raw
+
+if ($end2 != GLY) then
+echo D >> seq_raw
+endif
+
+
+set resnum = `grep -c "." seq_raw`
+
+echo System contains $resnum residues including dummy atoms.
+
+set i = 1
+set j = 1
+set seqq = ""
+rm seq
+while ($i <= $resnum)
+
+set aa = `head -$i seq_raw | tail -1`
+if ($aa == D) then
+set seqq = ${seqq}X
+else if ($aa == ALA) then
+set seqq = ${seqq}A
+else if ($aa == ARG) then
+set seqq = ${seqq}R
+else if ($aa == ASN) then
+set seqq = ${seqq}N
+else if ($aa == ASP) then
+set seqq = ${seqq}D
+else if ($aa == CYS) then
+set seqq = ${seqq}C
+else if ($aa == GLU) then
+set seqq = ${seqq}E
+else if ($aa == GLN) then
+set seqq = ${seqq}Q
+else if ($aa == GLY) then
+set seqq = ${seqq}G
+else if ($aa == HIS) then
+set seqq = ${seqq}H
+else if ($aa == ILE) then
+set seqq = ${seqq}I
+else if ($aa == LEU) then
+set seqq = ${seqq}L
+else if ($aa == LYS) then
+set seqq = ${seqq}K
+else if ($aa == MET) then
+set seqq = ${seqq}M
+else if ($aa == PHE) then
+set seqq = ${seqq}F
+else if ($aa == PRO) then
+set seqq = ${seqq}P
+else if ($aa == SER) then
+set seqq = ${seqq}S
+else if ($aa == THR) then
+set seqq = ${seqq}T
+else if ($aa == TRP) then
+set seqq = ${seqq}W
+else if ($aa == TYR) then
+set seqq = ${seqq}Y
+else if ($aa == VAL) then
+set seqq = ${seqq}V
+endif
+
+if ($j == 80) then
+echo $seqq >> seq
+set seqq = ""
+set j = 0
+endif
+
+set i = `echo $i + 1 | bc`
+set j = `echo $j + 1 | bc`
+end
+echo $seqq >> seq
+rm seq_raw
+
+set range1 = `echo $nstep2 / 2500 | bc | awk -F "." '{print $1}'`
+set range1 = `echo $range1 | bc`
+set div = `echo 12000 \* 10 / 24 | bc | awk -F "." '{print $1}'`
+set range0 = `echo $range1 - $div | bc | awk -F "." '{print $1}'`
+if ($range0 < 0 ) then
+set range0 = 10
+endif
+
+#echo $nstep2 $div
+echo WHAM will analyze range of snapshots from $range0 to $range1.
+
+sed "s/xxxxx/$box/g" wham_example.inp > wham.inp
+sed "s/XXX/$resnum/g" wham.inp > wham
+head -4 wham > wham.in
+grep -B 1 -A 999 "HOMOL_DIST" wham_example.inp > wham
+cat wham.in seq wham > wham.inp
+sed "s/BBB/$range0/g" wham.inp > wham
+sed "s/CCC/$range1/g" wham > wham.inp
+rm wham wham.in
+#qsub start_wham.mat
+
+
+################################################################################
+# Setting up and running cluster analysis
+echo "Setting up and running cluster analysis"
+
+sed "s/XXX/$resnum/g" cluster_example.inp > clust
+head -8 clust > clust.in
+grep -B 1 -A 999 "HOMOL_DIST" cluster_example.inp > clus
+cat clust.in seq clus > cluster.inp
+sed "s/nclust=ZZZ/nclust=$nclust/g" cluster.inp > clut
+sed "s/temper=AAA/temper=$temper/g" clut > cluster.inp
+rm clust clust.in clus
+#qsub start_cluster.mat
projects / unres.git / blobdiff