ADL: shall i add charges to the ligand?

yangyc@bii-sg.org yangyc at bii-sg.org
Fri Feb 25 06:55:33 PST 2005


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



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