Subject: ADT error message - "No Atom records"

From: Robert Flight <[email-masked]>
Date: Tue, 25 Mar 2003 11:49:25 -0400

Hi All,

I have been using AutoDockTools in Windows for a long time, and have had very 
few problems with it.  One of the major tasks I use it for is the conversion 
of my receptor Mol2 files to PDBQS files.  I am trying to use ADT in Linux, 
and I am getting the following error message:

The file /mnt/d_win/autodock/test_set/1gpn/tacl.gr3/02.1gpn.mol2 doesn't have 
Atom records, molecules can't be built
ERROR ************************************************
Traceback (innermost last):
  File 
"/usr/local/mgltools/rel.1.1beta/share/lib/python1.5/site-packages/ViewerFrame
work/VF.py", line 571, in tryto
    result = apply( command, args, kw )
  File 
"/usr/local/mgltools/rel.1.1beta/share/lib/python1.5/site-packages/AutoDockToo
ls/autogpfCommands.py", line 851, in doit
    mol = mols[0]
  File "/usr/local/mgltools/rel.1.1beta/share/lib/python1.5/UserList.py", line 
18, in __getitem__
    def __getitem__(self, i): return self.data[i]
IndexError: list index out of range

I have never seen the message "doesn't have Atom records" before, and as far 
as I can tell my Mol2 files look the exact same in Linux as they did in 
Windows, and I am using the same program to prepare them.  Any help or 
suggestions are very much appreciated.  I will summarise the responses to the 
list.

Thanks,

-Robert

********************************
Robert Flight
Masters Student
Department of Chemistry
University of New Brunswick
Fredericton, NB  Canada  E3B 6E2
e-mail: [email-masked]
 
********************************

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