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PostPosted: Wed Sep 24, 2014 12:48 pm 
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Joined: Wed Sep 24, 2014 12:36 pm
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Hi,

I would like to perform docking simulations for cyclodextrin / ligand complexes. When treating the cyclodextrin as rigid, I suceeded in generated the input files and running the docking via autodock 4.

However, I would like to treat part of the cyclodextrin as flexible (allowing the reorientation of hydroxyl side chains). I tried but I can't set up properly the receptor files. I got error message with prepare_flexreceptor4.py when applied to the cyclodextrin (while everything is OK with some protein files)

I wonder if it is possible to treat part of the receptor as flexible with non standard residus ? If yes, how to do so ?

Thanks in advance,

Best Regards,

Morgan


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