On Mar 29, 2010, at 12:48 PM, Eric Pettersen wrote:
A final possibility is to use the PubChem3D (<http://pubchem.ncbi.nlm.nih.gov/release3d.html
) files and convert them directly to Mol2 files. This would require the 1.5 release (the 1.4 series doesn't read the charges in the SDF file) and assumes that the included MMFF charges are sufficient for your needs and that the conformer provided is good enough for your purposes without minimization.
Just a short note regarding PubChem3D... as discussed previously, <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004766.html
you may not want to use their charges because functional groups such as amines and acids are in their neutral forms rather then the charged ones more likely at physiological pH. Elaine