From chemistry-request@server.ccl.net Tue Mar 25 10:53:14 2003 Received: from mailserv.unb.ca ([131.202.3.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2PFrEN19700 for ; Tue, 25 Mar 2003 10:53:14 -0500 Received: from pop.unb.ca (root@newpop.unb.ca [131.202.3.46]) by mailserv.unb.ca (8.12.6/8.12.6) with ESMTP id h2PFnQWw023116; Tue, 25 Mar 2003 11:49:26 -0400 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.11.6+Sun/8.11.6) with ESMTP id h2PFnPY22024; Tue, 25 Mar 2003 11:49:25 -0400 (AST) X-WebMail-UserID: l72k6 Date: Tue, 25 Mar 2003 11:49:25 -0400 Sender: Robert Flight From: Robert Flight To: AutoDockList , Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: ADT error message - "No Atom records" Message-ID: <3E97A363@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: 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: robert.flight@unb.ca ******************************** "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