[Chimera-users] adding an O in compound 1

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 18 09:59:16 PDT 2013

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:


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.
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 at 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.

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