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<div>This is actually a CHARMM thing rather than a VMD thing: in ILE, CD1 becomes CD for whatever reason. There are other naming mismatches - primarily in the hydrogens for protein and nucleic acids, but becoming more numerous as you get further off the beaten
track. </div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Tristan<br>
<br>
<div> </div>
<div> </div>
<div>Tristan Croll</div>
<div>Lecturer</div>
<div>Faculty of Health</div>
<div>School of Biomedical Sciences</div>
<div>Institute of Health and Biomedical Engineering</div>
<div>Queensland University of Technology</div>
<div>60 Musk Ave</div>
<div>Kelvin Grove QLD 4059 Australia</div>
<div>+61 7 3138 6443</div>
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<div><br>
On 1 Nov 2015, at 4:31 am, Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<br>
<br>
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<blockquote type="cite">
<div>Hi Smith,<br>
<br>
can you please send me the PDB file?<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 10/29/15 00:24, Smith Lee wrote:<br>
</div>
<blockquote cite="mid:428513313.1281048.1446103452309.JavaMail.yahoo@mail.yahoo.com" type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:16px">
<div id="yui_3_16_0_1_1446103033766_2530">Dear All,</div>
<div id="yui_3_16_0_1_1446103033766_2662"><br>
</div>
<div id="yui_3_16_0_1_1446103033766_2661">When I run phenix.real_space_refine, in the rotamer restraints step I meet the following error message:</div>
<div><br>
</div>
<div id="yui_3_16_0_1_1446103033766_2749">RuntimeError: rotatable bond atoms CG1-CD (as defined by tardy-tree): no match in rotamer-info.tor_ids
<br>
</div>
<div id="yui_3_16_0_1_1446103033766_2750"><br>
</div>
<div>Will you please let me know how to overcome this error?</div>
<div id="yui_3_16_0_1_1446103033766_2751"><br>
</div>
<div id="yui_3_16_0_1_1446103033766_2752" dir="ltr">Best regards.</div>
<div dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1446103033766_2753" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1446103033766_2748" dir="ltr">Smith<br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset> <br>
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