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PostPosted: Wed Oct 16, 2013 9:05 pm 
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When using the prepare_receptor4.py the only options I see is to use Gasteiger or leave the input charges. However, I would like to use Kollman charges (an option available via the GUI). Is there an other script or could this script be extended?

Thanks, regards,

Mihaly Mezei


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PostPosted: Thu Oct 17, 2013 9:40 pm 
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You could create a pdbqt file with Kollman charges using two scripts from AutoDockTools/Utilities24:

First create a pdbqs file for your molecule with prepare_receptor.py.
--The resulting pdbqs file will have Kollman charges that can be preserved by the pdbqs_to_pdbqt.py script used next if you include the -C flag (see below).

--here's the syntax I used to test this just now in my local MGLToolsPckgs directory.:
../bin/pythonsh AutoDockTools/Utilities24/prepare_receptor.py -r hsg1.pdb -A bonds_hydrogens -o oct17_hsg1

Here are the first 5 lines from the output file: oct17_hsg1.pdbqs:
Note in pdbqs format the third column in from the right holds the partial charge
ATOM 1 N PRO A 1 -5.322 -15.656 -12.341 1.00 38.10 0.017 9.00 -17.40
ATOM 2 HN1 PRO A 1 -4.966 -15.751 -11.390 1.00 0.00 0.333 0.00 0.00
ATOM 3 HN2 PRO A 1 -5.934 -16.471 -12.304 1.00 0.00 0.333 0.00 0.00
ATOM 4 CA PRO A 1 -4.275 -15.710 -13.408 1.00 40.62 0.142 9.40 4.00
ATOM 5 C PRO A 1 -2.894 -15.457 -12.807 1.00 42.64 0.526 9.82 4.00


THEN, use pdbqs_to_pdbqt.py to convert the pdbqs to pdbqt format
../bin/pythonsh AutoDockTools/Utilities24/pdbqs_to_pdbqt.py -s oct17_hsg1 -C

Here are the first 5 lines from the new output file: oct17_hsg1.pdbqt:
Note in pdbqt format the next-to-the-last column holds the partial charge
ATOM 1 N PRO A 1 -5.322 -15.656 -12.341 1.00 38.10 0.017 N
ATOM 2 HN1 PRO A 1 -4.966 -15.751 -11.390 1.00 0.00 0.333 HD
ATOM 3 HN2 PRO A 1 -5.934 -16.471 -12.304 1.00 0.00 0.333 HD
ATOM 4 CA PRO A 1 -4.275 -15.710 -13.408 1.00 40.62 0.142 C
ATOM 5 C PRO A 1 -2.894 -15.457 -12.807 1.00 42.64 0.526 C


Kollman charges from the pdbqs file are preserved in the pdbqt file because of the -C
flag.


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