The Molecular Graphics Laboratory Forum

Hi
I am trying to dock a list of 100 ligand molecules on a receptor molecule. I am running autodock vina from within cygwin installed in a windows machine. I tried to use the bash script as in the tutorial page :
#! /bin/bash

for f in ligand_*.pdbqt; do
b='basename $f .pdbqt'
echo Processing ligand $b
mkdir -p $b
vina --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt
done

------And my cygwin commnad was:
a)First i went into the directory:cd /cygdrive/c/Program\ Files/The\ Scripps\ Research\ Institute/vina
b)then used "./test.sh" to run the script.
c) vina.exe is in the same directory "vina"

-----It gave the following error.
./test.sh: line 2: $'r\r': command not found
./test.sh: line3:syntax error near unexpected token '$'do\r' '
'/test.sh: line3: 'for f in ligand_*.pdbqt; do


-----My conf file:
receptor = receptor.pdbqt

center_x = 2
center_y = 6
center_z = -7

size_x = 25
size_y = 25
size_z = 25

exhaustiveness = 8

The ligand file names: ligand_01.pdbqt etc
The ligand files and the bash script file are in the same directory(vina).

May i ask where i am going wrong.Will greatly appreciate your help.
Best Regards
saharinku