[Chimera-users] Fwd: CCL: hydroxide for dock

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 25 09:11:30 PDT 2007

Begin forwarded message:

> From: "Yubo Fan yubofan|-|mail.chem.tamu.edu" <owner- 
> chemistry at ccl.net>
> Date: July 25, 2007 7:50:36 AM PDT
> Subject: CCL: hydroxide for dock
> Reply-To: "CCL Subscribers" <chemistry at ccl.net>
> Hi, everyone,
> I'm preparing structures with Chimera for docking with Dock6. There  
> is a Zn-coordinating hydroxide that I want to keep in the  
> structure. When I prepare dock files, Chimera always treat it as a  
> water. Is there any way to define it as a hydroxide in Chimera?
> Thanks,
> Yubo
> ============================================================
> Dr. Yubo Fan               Email: yubofan_+_mail.chem.tamu.edu
> Department of Chemistry    Tel:   1-979-845-5237
> Texas A&M University
> College Station, TX 77843
> ============================================================

Dear Yubo,
I could answer more precisely if I could see the file, but without  
it, I recommend:

(a) looking at the residue name of the hydroxide in the text of the  
Is it WAT or HOH?  If so, you could edit it to a different name, say XOH
or HOM.

(b) then, run Dock Prep in Chimera including hydrogen addition and  
all the
steps before that (but don't assign charges or write the Mol2 file).

(c) check the structure; if hydrogen is added where you didn't want it,
simply delete it.  For example, Ctrl-click to select an atom and use
"Actions... Atoms/Bonds... delete" in the menu to delete it.

The protonation states are intended to be reasonable at physiological  
but if a group is expected to have a perturbed pKa (for example, in an
active site or near an ion), it is a good idea to check it and manually
add/delete hydrogens as needed. ( more details in

(d) run Dock Prep again with only the steps AFTER hydrogen addition
(charge assignment and Mol2 file output) turned on.  If it asks for the
net charge of XOH (or whatever you named it), indicate -1.

(e) that procedure will use Antechamber to calculate the partial  
charges on
the hydroxide O and H.  If, however, you already know the charges you  
to use for these atoms, you can edit the charge values in the output
Mol2 file.  In that case you wouldn't even have to go through all  
these steps,
but could simply also delete the extra hydrogen from the Mol2 file,  
if you can
figure out which line it is!  I just realized this last point, so it  
wasn't in
my original reply.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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