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Update README.md #1

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fdf491c
Update README.md
anjibabuIITK Mar 11, 2019
4e32033
script to choose hot atoms
anjibabuIITK Feb 5, 2021
afff4f4
Selects HOT atoms
anjibabuIITK Feb 6, 2021
a2802fd
Update Process_topology_REST2.sh
anjibabuIITK Feb 6, 2021
a98f558
fixed format issue
anjibabuIITK Feb 10, 2021
57dbc48
selection of range of residues are implemented
anjibabuIITK Feb 11, 2021
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15 changes: 4 additions & 11 deletions README.md
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Original file line number Diff line number Diff line change
@@ -1,17 +1,12 @@

**Enhaced_Sampling_Methods_Tutorials**
# Enhaced Sampling Methods Tutorials






* Molecular Dynamics(**MD**): Will be updated soon
* Molecular Dynamics(**MD**) : Will be updated soon
* Umbrella Sampling([**US**](https://github.com/NNairIITK/Enhanced_Sampling_Methods_Tutorials/tree/master/Umbrella_Sampling)) : will be updated soon
* Metadynamics([**METAD**](https://github.com/NNairIITK/Enhanced_Sampling_Methods_Tutorials/tree/master/Metadynamics)) : Will be updated soon
* Replica Exchange MD([**REMD**](https://github.com/NNairIITK/Enhanced_Sampling_Methods_Tutorials/tree/master/Replica_Exchange_MD))
: Updated
* Well Sliced Metadynamics(**WS-METAD**) : Will be updated soon
* Replica Exchange Solute Scaling([**REST2**](https://github.com/NNairIITK/Enhanced_Sampling_Methods_Tutorials/tree/master/REST2))
: Updated
* Temperature Accelerated Sliced Sampling([**TASS**](https://github.com/NNairIITK/Enhanced_Sampling_Methods_Tutorials/tree/master/TASS)) : Updated
Expand All @@ -20,10 +15,8 @@






** Keep looking at this page for more updates**

**Keep looking at this page for more updates**

Cheers !!!
Anji Babu
Expand Down
76 changes: 76 additions & 0 deletions REST2/Process_topology_REST2.sh
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#-------------------------------------------------------------------------------#
# Bash script to Process the topology for REST2 setup
# Selects the HOT atoms for REST2
#
# Author: Anji Babu Kapakayala
# IIT Kanpur, India.
#
# USAGE : bash Process_topology_REST2.sh topol.top
#
# Equilant command in vim: :%s/\%V /_/g
#
#-------------------------------------------------------------------------------#
#!/bin/bash
infile="$1"
#infile="trp_processed.top"
resid=0

#---> Setting output filename
fname=`echo "$infile"|cut -d "." -f1`
outfile="${fname}_hot.top"

#---> Make lines starts with * to ;*
sed -i "s/\*/;\*/g" $infile

while read line;do
#---->
res=`echo $line|awk '{print $2}'`
if [ "$res" == 'residue' ]
then
resid=`echo $line|awk '{print $3}'`
resid_ref=$resid
fi
#<---
resid_new=`echo $line|awk '{print $3}'`
if [ "$line" != "" ];then
if [ "$resid_new" != "" ];then
if [ "$resid_new" == "$resid_ref" ];then
C1=`echo $line|awk '{print $1}'`
C2=`echo $line|awk '{print $2}'`
C4=`echo $line|awk '{print $4}'`
C5=`echo $line|awk '{print $5}'`
C6=`echo $line|awk '{print $6}'`
C7=`echo $line|awk '{print $7}'`
C8=`echo $line|awk '{print $8}'`
C9=`echo $line|awk '{print $9}'`
C10=`echo $line|awk '{print $10}'`
C11=`echo $line|awk '{print $11}'`

if [ "$res" != 'residue' ] ;then
echo $C1$'\t'${C2}_$'\t'$resid_new$'\t'$C4$'\t'$C5$'\t'$C6$'\t'$C7$'\t'$C8$'\t'$C9$'\t'$C10$'\t' $C11 >> $outfile
else
echo "$line" >> $outfile
fi
else
echo "$line" >> $outfile
fi
else
echo "$line" >> $outfile
fi
else
echo "$line" >> $outfile
fi

first=`echo $line|awk '{print $1}'`
if [ "$first" == "[" ];then
#resid_new="X"
resid_ref="Y"
fi
done<$infile

#---> Make lines starts with ;* to *
sed -i "s/;\*/\*/g" $infile
sed -i "s/;\*/\*/g" $outfile
#---------------------------------------------------------#
# <========== ANJI BABU KAPAKAYALA ==========>
#---------------------------------------------------------#
119 changes: 119 additions & 0 deletions REST2/process_for_resid.sh
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@@ -0,0 +1,119 @@
#-------------------------------------------------------------------------------#
# Bash script to Process the topology for REST2 setup
# Selects the HOT atoms for REST2
#
# Author: Anji Babu Kapakayala
# IIT Kanpur, India.
#
# USAGE : bash Process_topology_REST2.sh topol.top
# bash process_topology_REST2.sh toptl.top --resid 1-5
#
# Equilant command in vim: :%s/\%V /_/g
#
#-------------------------------------------------------------------------------#
#!/bin/bash
infile="$1"
#infile="trp_processed.top"
resid=$3

#---> Setting output filename
fname=`echo "$infile"|cut -d "." -f1`
outfile="${fname}_hot.top"
touch $outfile

#---> Make lines starts with * to ;*
sed -i "s/\*/;\*/g" $infile

#-------------------------------------------------------------------------------#
function select_hot_atoms() {

while read line;do
echo "Processing for Resid: $resid"
#---->
res=`echo $line|awk '{print $2}'`
if [ "$res" == 'residue' ]
then
#--->
if [ "$1" == "all" ];then
resid=`echo $line|awk '{print $3}'`
resid_ref=$resid
else
resid_ref=$1
echo "Processing for Resid: $1"
fi
#<---
fi
#<---
resid_new=`echo $line|awk '{print $3}'`
if [ "$line" != "" ];then
if [ "$resid_new" != "" ];then
if [ "$resid_new" == "$resid_ref" ];then
C1=`echo $line|awk '{print $1}'`
C2=`echo $line|awk '{print $2}'`
C4=`echo $line|awk '{print $4}'`
C5=`echo $line|awk '{print $5}'`
C6=`echo $line|awk '{print $6}'`
C7=`echo $line|awk '{print $7}'`
C8=`echo $line|awk '{print $8}'`
C9=`echo $line|awk '{print $9}'`
C10=`echo $line|awk '{print $10}'`
C11=`echo $line|awk '{print $11}'`

if [ "$res" != 'residue' ] ;then
echo $C1$'\t'${C2}_$'\t'$resid_new$'\t'$C4$'\t'$C5$'\t'$C6$'\t'$C7$'\t'$C8$'\t'$C9$'\t'$C10$'\t' $C11 >> $outfile
else
echo "$line" >> $outfile
fi
else
echo "$line" >> $outfile
fi
else
echo "$line" >> $outfile
fi
else
echo "$line" >> $outfile
fi

first=`echo $line|awk '{print $1}'`
if [ "$first" == "[" ];then
#resid_new="X"
resid_ref="Y"
fi
done<$infile
}
#-------------------------------------------------------------------------------#
# <========================== MAIN CODE ====================================>
#-------------------------------------------------------------------------------#
if [ "$2" == "" ];then
echo "Processing All Residues"
select_hot_atoms all
else
case "$2" in
--resid|-r) echo "Resid : $resid"
if [ "$3" != "" ];then
r1=`echo $3|cut -d "-" -f1`
r2=`echo $3|cut -d "-" -f2`
echo "Initial Resid: $r1"
echo "Final Resid: $r2"
for i in `seq $r1 1 $r2`;do
select_hot_atoms $i
mv $outfile tmp
infile="tmp"
done

else
echo "Invalid resid.";exit
fi
;;
*) echo " Invalid Argument.";;
esac
fi

#-------------------------------------------------------------------------------#
#---> Make lines starts with ;* to *
sed -i "s/;\*/\*/g" $infile
sed -i "s/;\*/\*/g" $outfile
mv tmp $outfile
#-------------------------------------------------------------------------------#
# <========== ANJI BABU KAPAKAYALA ==========>
#-------------------------------------------------------------------------------#