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 Post subject: amino acids
PostPosted: Tue Jul 01, 2014 12:56 pm 
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Joined: Tue Jul 01, 2014 12:46 pm
Posts: 1
Dear users,


I am using AutoDock Vina by command line (./pythonsh
Utilities24/prepare_receptor4.py -r name_receptor) and my receptor is a peptide with
aminoacids like arginine,lysine, histidine,Glutamic Acid.

For example my peptide has a glutamic acid in a neutral form. But looking into the .pdbqt output, the charge of Glutamic Acid is -1 and it is wrong.

Is there any opportunities to set up an amino acids charged or neutral?
and set up the histidine protonation state?

How AutoDock manages these types of amino acids by default?

Thank you very much,

Mirko


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