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<div>Thank you, Eric!</div>
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<div>Do you know how do I save minimized file in a pdb format?</div>
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<div>I tried </div>
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<div>rc("minimize spec ':1-97.C z<10.0 & :.G|:1-97.C z<10.0 & :.F|:1-97.C' nsteps 100 cgsteps 0")</div>
<div>rc("write 'newfile.pdb'")</div>
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<div>It does the minimization, but doesn't write the file</div>
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<div><span style="color: rgb(255, 240, 165); font-family: Courier; font-size: 12px; background-color: rgb(19, 119, 62);">MidasError: "'newfile.pdb'" is not a model number</span></div>
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<div><span style="color: rgb(255, 240, 165); font-family: Courier; font-size: 12px; background-color: rgb(19, 119, 62);">Error while processing chimera_mini.py:</span>"</div>
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<div>Thank you!</div>
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<span style="font-weight:bold">From: </span>Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>><br>
<span style="font-weight:bold">Reply-To: </span>"<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
<span style="font-weight:bold">Date: </span>Monday, August 8, 2016 at 2:33 PM<br>
<span style="font-weight:bold">To: </span>"Bylund , Tatsiana (NIH/NIAID) [F]" <<a href="mailto:tatsiana.bylund@nih.gov">tatsiana.bylund@nih.gov</a>><br>
<span style="font-weight:bold">Cc: </span>"<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>" <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [Chimera-users] chimera minimize script<br>
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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>
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<div class="">—Eric</div>
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<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>
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<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>
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<div class="">Dear all,</div>
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</div>
<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>
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<span style="font-variant-ligatures: no-common-ligatures;" class=""></span><br 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>
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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>
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<span style="font-variant-ligatures: no-common-ligatures;" class="">Total charge for #0: 32.039</span></div>
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<span style="font-variant-ligatures: no-common-ligatures;" class="">Total charge for #0: 32.039</span></div>
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<span style="font-variant-ligatures: no-common-ligatures;" class=""></span><br class="">
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<span style="font-variant-ligatures: no-common-ligatures;" class="">The following residues had non-integral charges:</span></div>
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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>
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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>
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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>
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<span style="font-variant-ligatures: no-common-ligatures;" class=""></span><br class="">
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<span style="font-variant-ligatures: no-common-ligatures;" class="">1 model(s) had non-integral total charge</span></div>
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<span style="font-variant-ligatures: no-common-ligatures;" class="">Details in reply log</span></div>
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<span style="font-variant-ligatures: no-common-ligatures;" class="">Dock prep finished</span></div>
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<span style="font-variant-ligatures: no-common-ligatures;" class="">Error while processing chimera_mini.py:</span></div>
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<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="">
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<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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