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<p class="x_MsoNormal">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
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<p class="x_MsoNormal">‘Correct charges are unknown for 2 non-standard atom names in otherwise standard residues.</p>
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<p class="x_MsoNormal">Charges of 0.0 were assigned to the unknown atoms’</p>
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<p class="x_MsoNormal">In my protein< I did not remove two copper ions because my ligand will have to the two copper atoms after docking.</p>
<p class="x_MsoNormal">Please help me add the charges to my receptor.</p>
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<p class="x_MsoNormal">Thank you Sid</p>
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<p class="x_MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Wednesday, April 17, 2019 2:03:54 AM<br>
<b>To:</b> Sid Majaha<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu BB<br>
<b>Subject:</b> Re: [Chimera-users] Non-standard atom names</font>
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<div class="PlainText">Hi Sid,<br>
You should ask these questions on the DOCK-fans mailing list, not Chimera’s. See:<br>
<<a href="http://dock.compbio.ucsf.edu/Contact_Info/index.htm">http://dock.compbio.ucsf.edu/Contact_Info/index.htm</a>><br>
<br>
The DOCK website has tutorials, and license and download information for getting the program directly.<br>
<<a href="http://dock.compbio.ucsf.edu/">http://dock.compbio.ucsf.edu/</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
> On Apr 15, 2019, at 7:16 PM, Sid Majaha <sidumomajaha@live.com> wrote:<br>
> <br>
> Hi Eric<br>
> 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;<br>
> • Is there another way of using dock3.6 without using dock blaster?<br>
> • Is there another simpler tutorial for dock3.6 that you could recommend me to use?<br>
> • Are the dock 3.6 steps similar to the steps of dock6?<br>
> Sid<br>
<br>
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