[Chimera-users] Gasteiger charge

Ibrahim Moustafa I.moustafa at psu.edu
Thu Oct 13 13:29:44 PDT 2011

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 ³-4² on the ligand molecule.  However, the program
assigned partial charges that sum to total charge of ³-2² instead of ³-4².

  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.



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

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