add water and IONs

mkMu_04addWaterION.sh

#!/bin/sh
# GPL v. 3
# Program mkMu: 04addWaterION.sh
# 
#
# written by Naoyuki Miyashita 7/22/2014

#INPUT
inputPrefix="01_dd"
inpdcd="03.min/r.03.min.dcd"
outPrefix="04_addwt"
outPrefix2="04_ddng"
cons=0.15
SALT="POT"

numOfFrame=500

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

program="catdcd"

# OUT

#mk pdb from dcd
$program -otype pdb -o $outPrefix.pre.pdb \
-first $numOfFrame -last $numOfFrame \
-s $inputPrefix.psf -stype psf \
-dcd $inpdcd

line_1="package require solvate"
echo $line_1 > $outPrefix.inp
 
i=0
while [ $i -lt $numberOfTopology ]
do
topf=${topology[$i]}
line_1="topology $topf"
echo $line_1 >> $outPrefix.inp
i=$((i+1))
done

line_1="solvate $inputPrefix.psf $outPrefix.pre.pdb -t 15 -o $outPrefix"
echo $line_1 >> $outPrefix.inp
line_1="exit"
echo $line_1 >> $outPrefix.inp
vmd -dispdev text -e $outPrefix.inp > $outPrefix.log

##
line_1="package require autoionize"
echo $line_1 > $outPrefix2.inp
 
i=0
while [ $i -lt $numberOfTopology ]
do
topf=${topology[$i]}
line_1="topology $topf"
echo $line_1 >> $outPrefix2.inp
i=$((i+1))
done

line_1="autoionize -psf $outPrefix.psf -pdb $outPrefix.pdb -sc $cons -o $outPrefix2 -cation $SALT"
echo $line_1 >> $outPrefix2.inp
line_1="exit"
echo $line_1 >> $outPrefix2.inp
vmd -dispdev text -e $outPrefix2.inp > $outPrefix2.log

python maxmin.py $outPrefix2.pdb "all" > $outPrefix2.data