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Hello Chimera Software Developers,</div>
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I am having a lot of trouble coordinating a metal atom (using Zinc in place of Cr) to the nitrogen, oxygen, and potentially sulfur atom on cysteine. The two main problems that I am having are getting the geometry I need, which is octahedral, where the metal
is also coordinated to two-three water molecules as well as eventually the N-7 of guanine. I am trying to build and minimize the Zn-Cysteine model first though before incorporating it into a DNA oligo. I can't seem to get the geometry I need but beside from
that, I have tried to minimize the structure using Amber with an undesired geometry just to test if it will run, and it doesn't let me. I have read the reply log and I believe this is due to the atom labeling on cysteine being the issue. But changing the atoms
names is a coding problem, and I don't know anything about coding. I tried building cysteine on my own as a potential fix in place of using the prebuilt model but ran into the same problem where it would not minimize my structure. I need this model for my
dissertation, so any help would be greatly appreciated. I can attach any files that you may need, set up a zoom meeting, whatever is easiest for you. I know this is probably not the most conventional use for this software, but I really need to figure this
out, and I don't have enough knowledge to tinker with it on my own anymore. Thank you for any feedback.</div>
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Best Regards,</div>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 14pt;"><b>Sydney Marchi</b></span></div>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">PhD Candidate, Chemistry</span><br>
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Office: Shelby Hall, 3043</div>
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University of Alabama</div>
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