ADL: partail/formal charges from prepare_ligand4.py
mihaly.mezei at mssm.edu
Wed Apr 16 13:13:49 PDT 2014
I am using prepare_ligand4.py to set up ligands from a library of .mol2 files. However, I found that in some cases the partial charges don't sum up to an integral number; in other cases the formal charge is clearly wrong (the sum of the atomic numbers is an odd number but the forma charge is zero). I attached a small directory that contains some examples with the input .mol2 and output .pdbqt files (ligand CMOD131040 has partial charge sum = -1.5; the other ligands are all neutral but the atomic numbers sum up to an odd number).
The .pdbqt files were generated with the command
pythonsh $pythonutil/prepare_ligand4.py -v -l $mol2file -o $pdbqt
Am I doing something wrong, or is this a bug?
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