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.
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.
As Elaine says, the Mol2 type of the oxygen atoms in an oxygen molecule is O.2. In a structure with poor bond lengths, Chimera will sometimes guess that the oxygen molecule is instead a hydrogen peroxide, where the oxygens are O.3. --Eric On Jun 18, 2013, at 9:59 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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.
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participants (3)
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Elaine Meng -
Eric Pettersen -
Ibai Gazpio