Dear Chimera developers:

  I want to assign Gasteiger charges for a ligand, as a preparative step for docking.  The ligand is GTP, extracted from a protein complex structure.
 
  I wanted to add the Gasteiger partial charge, and explicitly chose to have a total charge of “-4” on the ligand molecule.  However, the program assigned partial charges that sum to total charge of “-2” instead of “-4”.

  Any idea why the program assigned the Gasteiger partial charges incorrectly, ignoring the input total charge on the ligand.

    Thanks in advance for your help.

  Regards,
 Ibrahim


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Ibrahim M. Moustafa, Ph.D.
Biochemistry and Molecular Biology Dept.
201 Althouse Lab., University Park,
Pennsylvania State University
PA 16802

Tel. (814) 863-8703
Fax (814) 865-7927