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I have some folders:

oldA with A_1.aaa, A_2.aaa, A_1.bbb, A.def, A.ghi 
oldB with B_1.aaa, B_2.aaa, B_1.bbb, B.def, B.ghi
and so on

and need to copy them to another folder with selection.

I want only A.def and A.ghi copy to /newA, so do with B. I have written a script but it doesn't work.

for i in A B C D
do
  folder="new${i}"
  mkdir $folder;
  cp path/to/old${i}/${i}{.def,.ghi} $folder
  cd $folder; some commands
  cd ..
done

The error is cp: cannot stat ‘oldA/A{.def,.ghi}’: No such file or directory

However, when I use direct command cp path/to/oldA/A{.def,.ghi} newA, it works well. What should I do?

If I want to copy only A_1.aaa and A_2.aaa, will the procedure be similar?

This is my actually script.

#!/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

Also, I have another problem in Konsole. I don't know whether it is relevant or not but I will post here too.

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  • 1
    Is that bash with brace expansion enabled? What is the output of echo $SHELL; echo $-? It should work your way. Indenpendent of your problem: You should use mkdir -p "$folder", cp "path/to/old${i}/${i}"{.def,.ghi} "$folder", and cd "$folder". – Hauke Laging May 21 '14 at 18:02
  • The outputs are /bin/bash and himBH. Your commands don't work. I think adding quotation marks don't make any changes. – Ooker May 21 '14 at 18:14
  • 1
    I told you in advance that these suggestions will not solve the problem. What is the shebang line of the script, #!/bin/bash? Have you executed echo $SHELL; echo $- in the script or in the shell which called the script? I suggest to reduce the code for approaching the problem. Put this single line in another script: i=A; echo "path/to/old${i}/${i}"{.def,.ghi} What is the output? – Hauke Laging May 21 '14 at 18:23
  • Yes, of course I have #!/bin/bash in top of the script. I executed on the shell called the script. When add to the old script, only /bin/bash/ appears, the line for echo $- is blank. The output of the new script is path/to/oldA/A"{.def,.ghi} – Ooker May 21 '14 at 18:35
  • That is really interesting. Please put set -B; echo $- before the i=A; echo "path/to/old${i}/${i}"{.def,.ghi} line and run the script again. – Hauke Laging May 21 '14 at 18:45
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It turns out that I use $ sh script to run the scrip, not $ bash script. The brace expansion requires bash to run.

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