Hello, An additional follow-up to Nancy's question from Jan 31. <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004754.html
Daily builds (version 1.5) dated Feb 4 or newer will now automatically read the partial charges in 3D SDF files obtained directly from the PubChem database. <http://pubchem.ncbi.nlm.nih.gov/release3d.html> However, I wanted to caution everybody that the protonation states of the resulting molecules are not what you would expect at physiological pH. The functional groups that would generally be charged near pH 7 are neutralized, at least from the few examples that I've examined: carboxylic and other acids fully protonated rather than formally negative, aliphatic amines neutral rather than formally positive. For example, alanine is given as H2N-CH(CH3)-COOH rather than + H3N- CH(CH3)-COO - If that is the case for all of the 3D SDFs obtained directly from PubChem (Nancy, you may want to take a closer look at a sample of your structures), I would not recommend them for docking. Instead, you may want to get small molecule structures from some place that has attempted to put them in reasonable charge states, such as the ZINC database. <http://zinc.docking.org/> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco