<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Tatsiana,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Residue 33 in chain K (an ASN) in your structure is missing the side chain. Since the first thing you do in your script is add hydrogens, Chimera adds two hydrogens to the carbon alpha of that residue. Since those hydrogens have no corresponding molecular mechanics parameters in the Amber database, the minimization didn’t work.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>You should not addh/addcharge in your script and instead run DockPrep. See this dock-fans posting for how to do that: <a href="http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html" class="">[Dock-fans] dock prep in batch mode?</a> That posting talks about adding keyword arguments you want to the prep() call. If you want to use Gasteiger charges, add “method=‘gasteiger’” to the call.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><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>
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<br class=""><div><blockquote type="cite" class=""><div class="">On Aug 8, 2016, at 10:06 AM, Bylund, Tatsiana (NIH/NIAID) [F] <<a href="mailto:tatsiana.bylund@nih.gov" class="">tatsiana.bylund@nih.gov</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div class="">Dear all,</div>
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<div class="">I need to minimize a lot of protein complexes and am trying to do it with a script. </div>
<div class="">I have a protein complex structure without Hydrogens, but when they are added in Chimera, it outputs error</div>
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<span style="font-variant-ligatures: no-common-ligatures;" class="">Non-standard atom names:</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 240, 165); background-color: rgb(19, 119, 62); min-height: 14px;" class="">
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<span style="font-variant-ligatures: no-common-ligatures;" class=""><span class="Apple-tab-span" style="white-space: pre;"></span>ASN HA2 (:33.K@HA2)</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 240, 165); background-color: rgb(19, 119, 62); min-height: 14px;" class="">
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<span style="font-variant-ligatures: no-common-ligatures;" class=""><span class="Apple-tab-span" style="white-space: pre;"></span>ASN HA3 (:33.K@HA3)</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 240, 165); background-color: rgb(19, 119, 62); min-height: 14px;" class="">
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<span style="font-variant-ligatures: no-common-ligatures;" class="">Total charge for #0: 32.039</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 240, 165); background-color: rgb(19, 119, 62); min-height: 14px;" class="">
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<span style="font-variant-ligatures: no-common-ligatures;" class="">Total charge for #0: 32.039</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 240, 165); background-color: rgb(19, 119, 62); min-height: 14px;" class="">
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<span style="font-variant-ligatures: no-common-ligatures;" class="">The following residues had non-integral charges:</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 240, 165); background-color: rgb(19, 119, 62); min-height: 14px;" class="">
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<span style="font-variant-ligatures: no-common-ligatures;" class=""><span class="Apple-tab-span" style="white-space: pre;"></span>:33.K 0.039</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 240, 165); background-color: rgb(19, 119, 62); min-height: 14px;" class="">
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<span style="font-variant-ligatures: no-common-ligatures;" class="">Correct charges are unknown for 2 non-standard atom names in otherwise standard residues</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 240, 165); background-color: rgb(19, 119, 62); min-height: 14px;" class="">
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<span style="font-variant-ligatures: no-common-ligatures;" class="">Charges of 0.0 were assigned to the unknown atoms</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 240, 165); background-color: rgb(19, 119, 62); min-height: 14px;" class="">
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<span style="font-variant-ligatures: no-common-ligatures;" class="">1 model(s) had non-integral total charge</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 240, 165); background-color: rgb(19, 119, 62);" class="">
<span style="font-variant-ligatures: no-common-ligatures;" class="">Details in reply log</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 240, 165); background-color: rgb(19, 119, 62); min-height: 14px;" class="">
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<span style="font-variant-ligatures: no-common-ligatures;" class="">Dock prep finished</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 240, 165); background-color: rgb(19, 119, 62); min-height: 14px;" class="">
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<span style="font-variant-ligatures: no-common-ligatures;" class="">Error while processing chimera_mini.py:</span></div><div style="margin: 0px; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 240, 165); background-color: rgb(19, 119, 62);" class="">
<span style="font-variant-ligatures: no-common-ligatures;" class="">No MMTK name for atom "HA3" in standard residue "ASN"</span></div>
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<div class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><br class="">
</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><br class="">
</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">When I delete residue K 33 (which DOES NOT have H in pub file) chimera runs minimization.</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><br class="">
</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">Would you have any suggestions?</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><br class="">
</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">Thank you!</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><br class="">
</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">Kind regards,</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">Tatsiana</span></div>
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