ADL: partail/formal charges from prepare_ligand4.py

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


Greetings,

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?

Best regards,

Mihaly Mezei

Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai
Voice:  (212) 659-5475   Fax: (212) 849-2456
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WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
WWW (Department): http://www.mssm.edu/departments-and-institutes/structural-and-chemical-biology
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