[Chimera-users] Non-standard atom names

[Sid Majaha]

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





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________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, April 17, 2019 2:03:54 AM
To: Sid Majaha
Cc: chimera-users at 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 at 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

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