<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Sheng,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera can definitely handle minimizing non-standard residues. There are various possibilities as to why it failed with your particular residue, but I would need more than the “failure running ANTECHAMBER” message to diagnose the problem. Could you repeat what you did and after you get the failure please use Help→Report A Bug to send a bug report to us? That will include the full contents of the Reply Log, which is what I need to see. Thanks.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On May 8, 2020, at 8:00 AM, Sheng Zhang <<a href="mailto:shengz4@uci.edu" class="">shengz4@uci.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="gmail_default" style="font-size:small">Dear UCSF Chimera team,</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">Good morning! I am Sheng Zhang, a graduate student from UC Irvine. First I would like to thank you for developing this useful tool, UCSF Chimera. I have a question regarding minimizing molecule with non-standard amino acids.</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">I modified a linear peptide ligand so it's now a ring containing non-standard amino acids. When I was trying to minimize the ligand while fixing its protein partner, I kept getting error messages like "failure running ANTECHAMBER for residue UNK+THR". The unknown and threonine residues happen to be the residues that I built and modified. Now they are no longer standard/intact amino acid residues and I guess that is why Chimera doesn't like them when trying to minimize the structure. </div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">I wonder is there a way to minimize ligand with non-standard amino acid groups? Thank you so much for your time and help!</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">Best wishes,</div><div class="gmail_default" style="font-size:small">Sheng</div></div>
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