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<p>Dear Elaine,</p>
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<p>Thank you for the respond.</p>
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<p>Yes I tried to overcome the problem with your suggestions but it didn't work. However I just deleted the whole metal ion complex and that solved the problem. Atleast it can be used as an visual suggestion for my future project.</p>
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<p>Best regards,</p>
<p>Elias Veijola<br>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>Lähettäjä:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Lähetetty:</b> 31. tammikuuta 2018 18:21:00<br>
<b>Vastaanottaja:</b> Veijola Elias<br>
<b>Kopio:</b> chimera-users@cgl.ucsf.edu<br>
<b>Aihe:</b> Re: [Chimera-users] VL: Minimizing the structure in Chimera</font>
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<div class="PlainText">Dear Elias Veijola,<br>
Sorry, there are only parameters for a certain set of elements.<br>
<br>
>From the Minimize Structure manual page:<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html</a>><br>
<br>
"Monatomic ions are assigned user-specified net charges and Amber VDW parameters. The following ions are handled: Li+, Na+, K+, Rb+, Cs+, F–, Cl–, Br–, I–, Mg2+, Ca2+, Zn2+. In addition, Fe ion nonbonded parameters are taken from the heme residue in the Amber
parameter database. See Limitations for how to add types.”<br>
<br>
It is very difficult to try to add parameters yourself, but you take a look at the Limitations section if you want:<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#limitations">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#limitations</a>><br>
<br>
If you are not trying to be highly precise or the Ni ion is not near the parts of interest, you could consider text-editing your input file to change it to a different metal (one in the list above) or even delete it entirely.<br>
<br>
Best regards,<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 Jan 31, 2018, at 2:16 AM, Veijola Elias <elias.veijola@aalto.fi> wrote:<br>
> Dear Mr. or Mrs.<br>
> I am trying to minimize a structure of mutated coEnzyme B but the program gives me this error
<br>
> Element Ni (atom #0:700.A@NI) is not currently supported [no GAFF type]<br>
> Best regards,<br>
> Elias Veijola<br>
<br>
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