ADL: Problem with "" ...

Abdessamad Ababou aa673 at
Mon Oct 31 02:15:56 PDT 2011

Dear Autodockers,


I'm doing virtual screening using Autodock-vina on about 200,000 small
molecules (sm). At the start of the run (few 1000 sm) I used the below
python script (I copy from the vina program webpage) and it worked. But now
reaching 40,000 sm the script doesn't work anymore and I got this errors


File "", line 23, in ?


File "", line 13, in doit

   Line = lines[1]

IndexError: list index out of range


Any help from you guys will be very much appreciated as I'm stuck to analyse
my results ... Many thanks for your time and help.


Best regards,





#! /usr/bin/env python


import sys

import glob


def doit(n):

    file_names = glob.glob('*.pdbqt')

    everything = []

    for file_name in file_names:

        file = open(file_name)

        lines = file.readlines()


        line = lines[1]

        result = float(line.split(':')[1].split()[0])

        everything.append([result, file_name])

    everything.sort(lambda x,y: cmp(x[0], y[0]))

    part = everything[:n]

    for p in part:

        print p[1],



if __name__ == '__main__':




More information about the autodock mailing list