make mutation for charm/namd by namd and vmd

mkMu_00mkMutation.sh

#!/bin/sh
# GPL v.3
# Program mkMu:   mkMutation.sh
# Naoyuki Miyashita 7/22/2014
# 

#
# Input

outfile="00_mutation1.inp"
initialPDB="input.pdb"
initialPSF="input.psf"
mkInputPrefix="00_mutation"
Outfile="00_mutant"

OutTempPrefix="00_tmp"

numberOfTopology=2
topology_0="../../par/top_prot_wation.rtf"
topology_1="../../par/top_all36_na.rtf"
topology=("$topology_0"  "$topology_1")

numberOfMutation=2
mutantSegment_0="P1"
mutantResID_0=333
mutantResname_0="ASP"
mutantSegment_1="P2"
mutantResID_1=444
mutantResname_1="GLU"

mutantSegment=("$mutantSegment_0" "$mutantSegment_1")
mutantResID=("$mutantResID_0" "$mutantResID_1")
mutantResname=("$mutantResname_0" "$mutantResname_1")

# runfile
#psfgen_cmd="#/home/miya/src/src_namd/NAMD_CVS-2013-02-26_Linux-x86_64-multicore-CUDA/psfgen << ENDMOL"
psfgen_cmd="#/home/miya/src/src_namd/NAMD_CVS-2013-04-08_Linux-x86_64-multicore/psfgen << ENDMOL"
vmd_cmd="~/bin/bin_vmd/vmd -dispdev text -e $Outfile.inp > $Outfile.log"


# make line
num=0
line_0="package require mutator"
echo $line_0  > $Outfile.inp
i=0
while [ $i -lt $numberOfTopology ]
do
topf=${topology[$i]}
line_1="topology $topf"
echo $line_1 >> $Outfile.inp
num=$((num+1))
i=$((i+1))
done

i=0

line_2="mutator -psf $initialPSF -pdb $initialPDB -o $OutTempPrefix$i -ressegname ${mutantSegment[$i]} -resid ${mutantResID[$i]} -mut ${mutantResname[$i]}"
echo $line_2 >> $Outfile.inp

i=$((i+1))
while [ $i -lt $numberOfMutation ]
do
pre=$((i-1))
line_2="mutator -psf $OutTempPrefix$pre.psf -pdb $OutTempPrefix$pre.pdb -o $OutTempPrefix$i -ressegname ${mutantSegment[$i]} -resid ${mutantResID[$i]} -mut ${mutantResname[$i]}"
echo $line_2 >> $Outfile.inp
num=$((num+1))
i=$((i+1))
done

line_3="exit"
echo $line_3 >> $Outfile.inp

# MK shel for PSFGEN
echo $psfgen_cmd > $Outfile.sh
echo $vmd_cmd    >> $Outfile.sh

# run command

sh $Outfile.sh
pre=$((i-1))
cp $OutTempPrefix$pre.pdb $Outfile.pdb
cp $OutTempPrefix$pre.psf $Outfile.psf
rm $OutTempPrefix*