ADL: ADT question --> merge non-polar hydrogens

Hatley, Jade M Jade.M.Hatley at uth.tmc.edu
Tue Mar 25 13:38:11 PDT 2008



Unfortunately, I cannot upgrade to AutoDock 4 in a manner timely for my project deadline (the IT dept is very scrict on downloads).  Other than upgrading, are there any suggestions for the cause of the error.  I have attached the apoprotein file that gives the error listed below (first email).
 
Thanks again,
Jade
________________________________
From: autodock-bounces at scripps.edu on behalf of Sargis Dallakyan
Sent: Mon 3/24/2008 4:15 PM
To: autodock at scripps.edu
Subject: Re: ADL: ADT question --> merge non-polar hydrogens

Hello Jade,

It seems that you are using an old version of ADT. Please upgrade to the latest
version of ADT-1.5.0: http://mgltools.scripps.edu/downloads

If the problem persists, send a bug report with apoprotein.pdb attached:
http://mgltools.scripps.edu/documentation/how-to/report-a-bug

Thanks,
Sargis


Jade Hatley wrote:
> Hello,
> I am trying to load a apoprotein .pdb into ADT in order to merge non-polar
> hydrogens, add charges, and save as .pdbqs.  The .pdb files were created by
> NAMD (I changed the appropriate amino acid aliases).  The protein is a P450
> and the I split them into an apoprotein.pdb file and a heme.pdb file.  It is
> the apo protein file that gives this error.  I've tried to search the
> tutorial and FAQs but cannot find anything specific.
>
> If anyone has any ideas or can point me to the section in a manual, I would
> really appreciate it.
>
> Jade

>>Python 2.3.2 (#6, Dec 11 2003, 15:11:30)
>>[GCC 2.95.3 20010315 (SuSE)] 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 1.0      ==== No Subprocess ====
>>
>>>>>ERROR ************************************************
>>
>>Traceback (most recent call last):
>>  File
>
> "/home/cheri/PROGRAMS/ADT/share/lib/python2.3/site-packages/ViewerFramework/VF.p
> y", line 582, in tryto
>
>>    result = apply( command, args, kw )
>>  File
>
> "/home/cheri/PROGRAMS/ADT/share/lib/python2.3/site-packages/Pmv/editCommands.py"
> , line 1975, in doit
>
>>    npHs = ats.get(lambda x: x.element=='H' and
>>  File
>
> "/home/cheri/PROGRAMS/ADT/share/lib/python2.3/site-packages/MolKit/tree.py",
> line 157, in get
>
>>    return self.ReturnType(filter(who, self.data))
>>  File
>
> "/home/cheri/PROGRAMS/ADT/share/lib/python2.3/site-packages/Pmv/editCommands.py"
> , line 1975, in <lambda>
>
>>    npHs = ats.get(lambda x: x.element=='H' and
>>  File "/home/cheri/PROGRAMS/ADT/share/lib/python2.3/UserList.py", line 28, in
>
> __getitem__
>
>>    def __getitem__(self, i): return self.data[i]
>>IndexError: list index out of range
>>
>
>
>
>
> -------------------------------
> Jade M. Hatley
> Graduate Student, PhD Candidate
> Biochemistry and Molecular Biology
> University of Texas - Houston Medical School
> MSB 3.316
> 713-500-6126
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---



-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: application/ms-tnef
Size: 4412 bytes
Desc: not available
Url : http://mgldev.scripps.edu/pipermail/autodock/attachments/20080325/6a5f716b/attachment.bin 


More information about the autodock mailing list