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PostPosted: Wed Jul 31, 2013 10:05 am 
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Any idea how to run Autodock with the python scripts
i need add Hydrogen atoms to ligand but i cannot do it with the front end of ADT4.2 so i got suggestions to run prepare_ligand4.py from MGLtools ADT4.2 and i need to know where to place the ligand name in Prepare_ligand4.py script. Any Idea??


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PostPosted: Wed Sep 25, 2013 12:53 pm 
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you have to execute the script with the ligand_name in arguments of the command line as follows:
python prepare_ligand4.py -l ligand_name -v

if you want to automatize the process you have to re-write the piece of code corresponding to the command line.

you need to understand how the python 'getopt()' function work: http://pymotw.com/2/getopt/


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