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PostPosted: Fri Apr 25, 2014 10:42 am 
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Joined: Wed Sep 11, 2013 10:14 am
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Hi,
I don't know if you realize, but after charges calculation by other program I try to put (and preserve) the ligand file in format mol2 in autodocktools for generating the pdbqt.
Although it appeares the message that the charges have been preserved indeed they were been changed.


I tried also to prepare manually the ligand through the scripts prepare_ligand.py and prepare_ligand4.py (with the -C option), but the result is the same.

How can I solve this problem?


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PostPosted: Fri Apr 25, 2014 10:35 pm 
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If your mol2 file contains any non-polar hydrogens, the charges on the carbons to which these atoms are bound will change when written in pdbqt format. This happens because autodock uses a united-atom representation, modelling only polar hydrogens.

United atom representations are obtained by first computing the partial charges for an all-hydrogen model of the molecule. Next, the charge on each hydrogen atom bonded to a non-polar heavy atom (eg a carbon atom) is added to the charge of the heavy atom and the hydrogen atom itself is removed from the molecule. (http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file/?searchterm=united-atom)

If the charges on other atoms have changed between your mol2 file and the new pdbqt file, you may have uncovered a new bug so it would be very helpful if your would provide your files (mol2 + pdbqt)....


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