ADL: partail/formal charges from

Mezei, Mihaly mihaly.mezei at
Wed Apr 16 13:13:49 PDT 2014


I am using 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/ -v -l $mol2file -o $pdbqt 

Am I doing something wrong, or is this a bug?

Best regards,

Mihaly Mezei

Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai
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