ADL: how to increase torsion freedom in autodock4

mswingle at jaguar1.usouthal.edu mswingle at jaguar1.usouthal.edu
Wed Oct 24 00:54:59 PDT 2007


Hi Hairat,

What does your docking log file look like? 

Mark

----- Original Message -----
From: Hairat Sabit <hairat at hotmail.com>
Date: Wednesday, October 24, 2007 2:31 am
Subject: ADL: how to increase torsion freedom in autodock4
To: autodock at scripps.edu


> Hi, all
>  
> In order to increase the limit set for torsion freedom (which is set 
> to 32), we went back to binary source code.  We increased MAX_TREES in 
> line 109, and MAX_TORS 32 in line 110; however, when test it, it 
> failed and gave the following error message.  If we change it back to 
> original value, the program is fine.
>  
> Any suggestion on this and how technically we should do it would be 
> very helpful.  And, is ther programming error in their checking code?
>  
> Thank you so much in advance,
>  
> Hairat
>  
> The error message is:
>  
> 
======================================================================
> ERROR: Check the final energy is expected value.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "./test_autodock4.py", line 136, in test_check_result_energy
>     (intermol_energy, internal_energy) = parse_energy_from_DLG( 
> self.dlg_filename )
>   File "./test_autodock4.py", line 98, in parse_energy_from_DLG
>     docked = parser.clist[0]  #dictionary of results
> IndexError: list index out of range
> 
> 
======================================================================
> ERROR: check the final energy is expected value
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "./test_autodock4.py", line 158, in test_check_result_energy_default_parameter_file
>     (intermol_energy, internal_energy) = parse_energy_from_DLG( 
> self.dlg_filename )
>   File "./test_autodock4.py", line 98, in parse_energy_from_DLG
>     docked = parser.clist[0]  #dictionary of results
> IndexError: list index out of range
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