Hi Ibai, If you are asking what atom type GOLD will accept, I recommend asking the GOLD developers. All I can say is that O.3 is one of the commonly used atom types in the mol2 format, as listed here: <http://www.tripos.com/mol2/atom_types.html> Looking at diagrams of Compound I, I would guess O.2 instead, but that is based purely on chemistry. I don't know anything about the input requirements of GOLD. 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 On Jun 17, 2013, at 10:28 AM, Ibai Gazpio <ibaigazpio@gmail.com> wrote:
Hi all, I'm trying to add an O molecule as compound 1 bound to a Fe of an Hem group. I use a program called GOLD to perform dockings but this doesn't recognize this O atom type, that is a O.3 type.. The output should be a mol2 file. Which atom type should I use? Ibai.