Hello. I am using the tyrosinase protein, 2Y9W for docking but I am having some difficulties using chimera. I want to prepare docking by adding hydrogen and charges but its giving me an error message of ‘Correct charges are unknown for 2 non-standard atom names in otherwise standard residues. Charges of 0.0 were assigned to the unknown atoms’ In my protein< I did not remove two copper ions because my ligand will have to the two copper atoms after docking. Please help me add the charges to my receptor. Thank you Sid Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, April 17, 2019 2:03:54 AM To: Sid Majaha Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Non-standard atom names Hi Sid, You should ask these questions on the DOCK-fans mailing list, not Chimera’s. See: <http://dock.compbio.ucsf.edu/Contact_Info/index.htm> The DOCK website has tutorials, and license and download information for getting the program directly. <http://dock.compbio.ucsf.edu/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 15, 2019, at 7:16 PM, Sid Majaha <sidumomajaha@live.com> wrote:
Hi Eric So I have been only using dock6 for docking and now want to venture in using dock3. I tried checking online for tutorials that I could look at but there are just a couple of them. On the UCSF website, there is a tutorial but requires the use of dock blaster. I just have a few questions; • Is there another way of using dock3.6 without using dock blaster? • Is there another simpler tutorial for dock3.6 that you could recommend me to use? • Are the dock 3.6 steps similar to the steps of dock6? Sid