ADL: charged ligands/Gasteiger?

Mihaly Mezei Mihaly.Mezei at mssm.edu
Fri Nov 11 14:58:32 PST 2011


Hello, Ruth,

I am trying to use prepare_ligand4.py to create a .pdbqt file from a .pdb file that came out of a screening with DOCK. It seems to work, in the sense that I get a file with the various torsion directives, as expected from a pdbqt file.

What would be ideal is that the Gasteiger charge generation could take into account the total charge, but I don't see any option that allows me to tell prepare_ligand4.py the total charge. Absent that possibility, does prepare_ligand4.py read the charges from a pdb file? That file has charges in the temperature factor column and also a record for the total charge.

Sorry for pestering you with my wishes.

Best,
Mihaly 

Mezei

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