[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:

<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 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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