3B7V.sh

#!/bin/bash
folder="Disperse"
mkdir $folder
cp 3B7V.pdb $folder
cd $folder

#awk '$5 != "C"' 3B7V.pdb > 3B7V_temp.pdb
#awk '$4 != "C"' 3B7V_temp.pdb > AB.pdb
sed -n 403,1981p 3B7V.pdb > A.pdb
sed -n 1982,3586p 3B7V.pdb > B.pdb

cd ..;mkdir EM;cd EM
for i in A B
do
  folder="${i}_EM"
  mkdir $folder
  cp ../em.mdp ../Disperse/${i}.pdb $folder
  cd $folder

  echo -e "\n4" | pdb2gmx -f ${i}.pdb -o ${i}.gro -water none
  grompp -f em.mdp -c ${i}.gro -p topol.top -o ${i}_em.tpr
  mdrun -v -deffnm ${i}_em
  #grompp -f em.mdp -c ${i}_em.gro -p topol.top -o ${i}_em_mead.tpr
  cd .. #at EM folder
done

cd ..;mkdir PQR;cd PQR
for i in A B
do
  folder="${i}_PQR"
  mkdir $folder
  cp ../EM/${i}_EM/${i}* $folder
  cd $folder

  editconf -f ${i}_em.gro -o ${i}_em.pdb
  awk '$1 != "REMARK"' ${i}_em.pdb > ${i}_temp.pdb
  pdb2pqr --ff=AMBER --apbs-input ${i}_temp.pdb ${i}.pqr -v > log_${i}
  #editconf -f ${i}_em_mead.tpr -mead ${i}_gro.pqr
  #for j in *.pqr; do sed 1,8d "$j" > ../"${j/.*}"_sed.pqr; done
  cd .. #at PQR folder
done

cd ..;mkdir APBS;cd APBS
for i in A B
do
  folder="${i}_APBS"
  mkdir $folder;ls
  cp ../PQR/${i}_PQR/${i}{.pqr,.in} $folder
  cd $folder

  abps ${i}.in
  cd .. #at APBS folder
done