ADL: shall i add charges to the ligand?

Susan Heffron sheffron at
Fri Feb 25 10:52:11 PST 2005

Dear Yuchen,

I believe that it is best to add the formal charge to the ligand (on
the appropriate atom) before converting it from 2D to 3D.  That is
what has worked best for me with ICM.

                      Susan Heffron

yangyc at wrote:
> Dear all,
> I am trying to generate 3D coordinates for a set of small molecules using
> ICM. Some ligands do have net charges, for example, certain ligand has a
> positive charge on the N atom. Therefore, after converting the 2D
> coordinates to 3D (in mol2 format), do i have to add charges to these
> small molecule, as i feel this may affect the docking results.
> Thanks!
> Best Regards,
> yuchen
> ________________________________________________
> --- ADL: AutoDock List  --- ---

        Susan Heffron
Dept. of Physiology and Biophysics                               
University of California, Irvine                
 Irvine, CA  92697-4560   U.S.A.                         
    phone:  (949) 824-4625
    FAX:    (949) 824-8540

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