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My favorite is the elbow builder in phenix. You give it a "smiles" string and it will build (and optionally, optimize either classically or quantum-mechanically) your small molecule structure. http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification http://www.phenix-online.org/documentation/elbow.htm You can also build one using a "smiles" string in coot. http://www.msg.ucsf.edu/local/programs/coot/user-manual.html#SEC112 On Jul 22, 2008, at 1:42 PM, Ariel Talavera wrote: > Hi all, > > I need to create the coordinates of a small molecule with no > structure yet. Could any one tell me what program can I use to build > small molecules? > > Thanks in advamced. > > Ariel > > -- > Ariel Talavera, Lic. > Dept. of Computational and Structural Biology > Center of Molecular Immunology > P.O.Box 16040, Havana 11600 > Cuba > tel: (53-7) 271 7933, ext. 219 > fax: (53-7) 272 0644 > email: [log in to unmask]