Shell Programming and Scripting

I am working with autodock vina for virtual screening and docking with cygwin. Autodock vina generates conformers for multiple ligands. I want to make the complex of these conformers with receptor. e.g. I have 100 .pdbqt files form vina output and one receptor pdbqt file. By running command-

Code:

cut -c-66 inh*.pdbqt > inh*.pdb

I can convert inh*.pdbqt to pdb, but I have to do this individually for all ligands (* here are random numbers from pubchem database).

With command-

Code:

cat Receptor.pdbqt  inh*.pdb | grep -v '^END ' | grep -v '^END$' > complex.pdb

With this command the pdb of complex of receptor and ligand is generated, but again this I have to do for each ligand, receptor file is fixed in this case.

I want a bash script for above to commands to run in cygwin. Aim is to use multiple ligand files - convert them to pdb - merge with receptor.pdbqt - generate multiple complexes as per ligand names.

This may need a simple script. Though I have worked with many scripts I don't know how to write such bash scripts. Naively, I have given a try and wrote one script-

Code:

#!/bin/bash
for f in inh*.pdbqt; do b=`basename $f .pdbqt`;

$b; mkdir -p data02; cut -c-66 inh*.pdbqt > inh*.pdb;

cat 3V3VN.pdbqt inh*.pdb | grep -v '^END' | grep -v '^END$' > complex*.pdb;

$f --out data02/$f.pdbqt --log data02/$f.txt; done

It generates the complex but only one complex with all ligands in it !!!

I'm afraid I can't deal with receptors nor ligands. How about posting the input files and desired output?