Subject: ADT error message - "No Atom records" - solution

From: Robert Flight <[email-masked]>
Date: Tue, 25 Mar 2003 17:04:10 -0400

Thanks to everyone to tried to help me with this, your suggestions were 
appreciated.  I did figure out what was wrong, or at least a solution.  I am 
running a dual boot machine with RHLinux7.3 and WindowsXP.  I have a FAT32 
drive partition so I can write and read it in both Linux and XP.

It turns out that ADT in Linux does not like mol2 files that were created in 
XP, it gives me the error message I reported below.  If I create the Mol2 file 
in Linux, ADT gives me no problems.  I guess I should have tried that first, 
but I could not find any obvious differences between files that worked and 
files that didnt.  A good lesson to work in one operating system or the other, 
not both.

-Robert

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]

********************************

"A computer terminal is not some clunky old television with a typewriter in 
front of it.  It is an interface where the mind and body can connect with the 
universe and move bits of it about." -- Hitch Hikers Guide to the Galaxy

-- ADL: AutoDock List  --- http://www.scripps.edu/pub/olson-web/doc/autodock/ 
---

---

From: Craig Shepherd <[email-masked]>
Date: Tue, 25 Mar 2003 15:42:07 -0700

Hi there,

Sounds like you don't have a problem any more, but I think
I know what MIGHT have caused it.  Text files created on a Windows
operating system contain both "newlines" and "carriage returns"
at the end of lines, whereas those made on *nix OS's have just newlines. 
I first noticed this with PostScript files I opened up in Emacs on my
linux partition (I had made them with Illustrator). In this case, you'll 
see
a "^M" at the end of every line.

You can interconvert text files between DOS and *nix if you install
the package "tofrodos" on your linux partition.  It provides the program
"fromdos", which will strip (or add) the carriage returns as needed.
You can find the package at http://rpmfind.net

Hope that helps if you ever face this kind of thing again.

Craig Shepherd

---

From: "Lubos Vrbka" <[email-masked]>
Date: Tue, 25 Mar 2003 22:34:23 +0100

hi,

try using unix shell scripts that are attached - to_dos converts unix text
files to windows text files; to_unix does the opposite conversion - it just
removes ^M characters that are appended to the end of line in all text files
in dos/windows...

syntax is
to_dos unix_file_name dos_file_name
to_unix dos_file_name unix_file_name

the problem could be in these ^M characters... vi should display them, but
i'm not sure about other editors/viewers... and a question is if they
are/aren't interpreted in autodock somehow... try, it could help and surely
won't hurt... :o)

regards,
lubos

-
#################################################
Lubos Vrbka
National Centre for Biomolecular Research
Masaryk university, Brno, Czech Republic

[email-masked]
http://www.chemi.muni.cz/~shnek
tel. +420 541 129 508
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