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From: "Yubo Fan yubofan|-|mail.chem.tamu.edu" <owner- chemistry@ccl.net> Date: July 25, 2007 7:50:36 AM PDT Subject: CCL: hydroxide for dock Reply-To: "CCL Subscribers" <chemistry@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 seeing it, I recommend: (a) looking at the residue name of the hydroxide in the text of the file. 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 pH, 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 http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ dockprep.html ) (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 want 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 ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html