1) install autodocktools and use pdbqt_to_pdb to convert the files.

2) the command "updatedb ; locate pdbqt_to_pdb.py" will allow you to find the executable.Alternatively you can use babel (http://openbabel.org/docs/dev/FileFormats/AutoDock_PDQBT_format.html)

3) Take care about line n°4 of the following script and execute it (hope you're using linux).

----------------------------------BEGINNING OF THE SCRIPT------------------------

#CREATE A WORKING DIR

mkdir pdbs

# CONVERT THE PDBQTs into PDB and put them in the pdbs directory

for file in *.pdbqt

do

pdbqt_to_pdb.py -f $file

done

mv *.pdb pdbs/

#goes inside the directory and, for every file it generates a complex

#named 3VNDN_[the name of the ligand].pdb

cd pdbs

for file in in*.pdb

do

b=basename $file .pdb

cat 3V3VN.pdb | grep -v END > 3VNVN_$b.pdb

echo TER >> 3VNVN_$file.pdb

cat $file | grep HETATM >> 3VNVN_$b.pdb

echo END >> 3VNVN_$b.pdb

done

----------------------------------END OF THE SCRIPT------------------------

check the names, try it and let me know.

I am a little confused about what you wrote. If you just want to use BASH to do repeated job, I suggest you use LIST to do it as below.

#!/bin/bash

file_list=`ls -lrtx1 *.pdbqt'

for i in $file_list

do

cut -c-66 $i > $i.pdb

done

Your query is little difficult to understand as mentioned by Dr.Sun. If you just want to make the script automatic the simplest way is to use a for loop. e.g.

#!/bin/sh

for ((i=0;i inh$i.pdb

rm \#* 

done;

This simply will automate the total .pdbqt files to .pdb files. You can also write the output files in a different directory by specifying the working directory as described below.

#!/bin/sh

path=/user/~/~/~

cd $path

Best regards

Bikash, Osaka Univ.