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 Post subject: ADT ERROR
PostPosted: Sun Oct 11, 2009 11:08 pm 
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Joined: Sun Oct 11, 2009 10:58 pm
Posts: 1
Hello,

I am trying to run autodock with ADT on a linux box. However, I get this error message when I try to write or save a pdb.


Python 2.5.1 (r251:54863, Sep 21 2007, 11:20:07)
[GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-56)] on linux2
Type "copyright", "credits" or "license()" for more information.

****************************************************************
Personal firewall software may warn about the connection IDLE
makes to its subprocess using this computer's internal loopback
interface. This connection is not visible on any external
interface and no data is sent to or received from the Internet.
****************************************************************

IDLE 1.2.1 ==== No Subprocess ====
>>> ERROR *********************************************
Traceback (most recent call last):
File "/home/neville/MGLTools-1.5.4/MGLToolsPckgs/ViewerFramework/VF.py", line 735, in tryto
result = apply( command, args, kw )
File "/home/neville/MGLTools-1.5.4/MGLToolsPckgs/Pmv/fileCommands.py", line 1209, in doit
bondOrigin=bondOrigin, ssOrigin=ssOrigin)
File "/home/neville/MGLTools-1.5.4/MGLToolsPckgs/MolKit/pdbWriter.py", line 139, in write
file = open(filename, 'w')
IOError: [Errno 13] Permission denied: '/home/neville/5htclo/auttut/tutorial4/hsg1.pdb'


Also If I ignore the above and still prepare all the files and run autodock to completion. I still cannot analyze the results because It cannot let me open the .dlg file

This is what I get when I attempt to open one.

Python 2.5.1 (r251:54863, Sep 21 2007, 11:20:07)
[GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-56)] on linux2
Type "copyright", "credits" or "license()" for more information.

****************************************************************
Personal firewall software may warn about the connection IDLE
makes to its subprocess using this computer's internal loopback
interface. This connection is not visible on any external
interface and no data is sent to or received from the Internet.
****************************************************************

IDLE 1.2.1 ==== No Subprocess ====
>>> ERROR *********************************************
Traceback (most recent call last):
File "/home/neville/MGLTools-1.5.4/MGLToolsPckgs/ViewerFramework/VF.py", line 735, in tryto
result = apply( command, args, kw )
File "/home/neville/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/autoanalyzeCommands.py", line 2848, in doit
d.readDlg(dlgFile)
File "/home/neville/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/Docking.py", line 74, in readDlg
dlo = DockingLogObject(self, dlgFile)
File "/home/neville/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/Docking.py", line 337, in __init__
parser.parse(filename)
File "/home/neville/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/DlgParser.py", line 106, in parse
self.match(allLines)
File "/home/neville/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/DlgParser.py", line 219, in match
apply(d['func'], (lines,), {})
File "/home/neville/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/DlgParser.py", line 696, in getModelLines
self.makeModels(modelList)
File "/home/neville/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/DlgParser.py", line 792, in makeModels
clist.append(self.makeModel(curMod))
File "/home/neville/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/DlgParser.py", line 886, in makeModel
d['unbound_energy'] = float((ll)[6])
ValueError: invalid literal for float(): =


Will appreciate any hints and help on how to tackle this issue.
Thanks
dalemu


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