<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=""><div class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 1, 2019, at 3:33 PM, Thomas Evangelidis <<a href="mailto:tevang3@gmail.com" class="">tevang3@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class="gmail_default" style="font-size: large;"><pre style="font-family:"DejaVu Sans Mono";font-size:12.8pt" class=""><span style="color:rgb(0,0,128);font-weight:bold" class="">import </span>chimera<br class=""><span style="color:rgb(0,0,128);font-weight:bold" class="">from </span>Addions <span style="color:rgb(0,0,128);font-weight:bold" class="">import </span>initiateAddions<br class=""><span style="color:rgb(0,0,128);font-weight:bold" class="">from </span>DockPrep <span style="color:rgb(0,0,128);font-weight:bold" class="">import </span>prep</pre><pre style="font-family:"DejaVu Sans Mono";font-size:12.8pt" class="">models = chimera.openModels.list(<span style="color:rgb(102,0,153)" class="">modelTypes</span>=[chimera.Molecule])<br class=""><span style="color:rgb(0,0,128);font-weight:bold" class="">print </span><span style="color:rgb(0,128,0);font-weight:bold" class="">"Preparing receptor for docking and calculating ligand AM1 charges (may be slow)."<br class=""></span>prep(models, <span style="color:rgb(102,0,153)" class="">nogui</span>=<span style="color:rgb(0,0,128)" class="">True</span>, <span style="color:rgb(102,0,153)" class="">method</span>=<span style="color:rgb(0,128,0);font-weight:bold" class="">'am1'</span>)</pre><pre style="font-family:"DejaVu Sans Mono";font-size:12.8pt" class=""># and after I change the protonations</pre><pre style="font-family:"DejaVu Sans Mono";font-size:12.8pt" class="">rc(<span style="color:rgb(0,128,0);font-weight:bold" class="">"addcharge std spec #0"</span>) <span style="color:rgb(128,128,128);font-style:italic" class=""># re-add ff14SB charges to the protonated receptor only (the ligand protonation did not change)</span></pre><pre style="font-family:"DejaVu Sans Mono";font-size:12.8pt" class="">initiateAddions(models, <span style="color:rgb(0,128,0);font-weight:bold" class="">"Cl-"</span>, <span style="color:rgb(0,128,0);font-weight:bold" class="">"neutralize"</span>, chimera.replyobj.status)<br class=""></pre><pre style="font-family:"DejaVu Sans Mono";font-size:12.8pt" class=""><span style="color:rgb(128,128,128);font-style:italic" class=""><br class=""></span></pre></div></div></div></div></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, 2 Apr 2019 at 00:23, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word" class="">Hi Thomas,<div class=""><span class="gmail-m_-3318704790743477738Apple-tab-span" style="white-space:pre-wrap"> </span>Addcharge is what adds GAFF types. What exact addcharge command or function call are you using?</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Apr 1, 2019, at 2:25 PM, Thomas Evangelidis <<a href="mailto:tevang3@gmail.com" target="_blank" class="">tevang3@gmail.com</a>> wrote:</div><br class="gmail-m_-3318704790743477738Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class="gmail_default" style="font-size:large">Hi Eric,</div><div class="gmail_default" style="font-size:large"><br class=""></div><div class="gmail_default" style="font-size:large">Thanks, but it seems that it doesn't recognize one of ligand's hydrogens, which is strange because I calculate AM1 charges before adding ions. This is the whole error message. I also attach the input files. Do you have any idea about what might be wrong?</div><div class="gmail_default" style="font-size:large"><br class=""></div><div class="gmail_default" style="font-size:large"><div class="gmail_default">Traceback (most recent call last):</div><div class="gmail_default"> File "/home/thomas/Programs/Anaconda2/envs/ete3/bin/pychimera", line 12, in <module></div><div class="gmail_default"> update_dict = pychimera.__main__.run()</div><div class="gmail_default"> File "/home/thomas/Programs/Anaconda2/envs/ete3/lib/python2.7/site-packages/pychimera/__main__.py", line 6, in run</div><div class="gmail_default"> pychimera.main()</div><div class="gmail_default"> File "/home/thomas/Programs/Anaconda2/envs/ete3/lib/python2.7/site-packages/pychimera/core.py", line 347, in main</div><div class="gmail_default"> run_cli_options(args)</div><div class="gmail_default"> File "/home/thomas/Programs/Anaconda2/envs/ete3/lib/python2.7/site-packages/pychimera/core.py", line 309, in run_cli_options</div><div class="gmail_default"> globals().update(runpy.run_path(choice, run_name="__main__"))</div><div class="gmail_default"> File "/home/thomas/Programs/Anaconda2/envs/ete3/lib/python2.7/runpy.py", line 252, in run_path</div><div class="gmail_default"> return _run_module_code(code, init_globals, run_name, path_name)</div><div class="gmail_default"> File "/home/thomas/Programs/Anaconda2/envs/ete3/lib/python2.7/runpy.py", line 82, in _run_module_code</div><div class="gmail_default"> mod_name, mod_fname, mod_loader, pkg_name)</div><div class="gmail_default"> File "/home/thomas/Programs/Anaconda2/envs/ete3/lib/python2.7/runpy.py", line 72, in _run_code</div><div class="gmail_default"> exec code in run_globals</div><div class="gmail_default"> File "/usr/local/bin/protonate_receptor.py", line 300, in <module></div><div class="gmail_default"> write_protonated_structure(protonations)</div><div class="gmail_default"> File "/usr/local/bin/protonate_receptor.py", line 129, in write_protonated_structure</div><div class="gmail_default"> initiateAddions(models, "Cl-", "neutralize", chimera.replyobj.status)</div><div class="gmail_default"> File "/home/thomas/Programs/Chimera/share/Addions/__init__.py", line 72, in initiateAddions</div><div class="gmail_default"> noGaffComplain(noGaff, "Add Ions")</div><div class="gmail_default"> File "/home/thomas/Programs/Chimera/share/WritePrmtop/__init__.py", line 10, in noGaffComplain</div><div class="gmail_default"> raise ValueError("Cannot determine GAFF type for %s (etc.)" % noGaff[0])</div><div class="gmail_default">ValueError: Cannot determine GAFF type for #1:1@H1 (etc.)</div><div class=""><br class=""></div></div><div class="gmail_default" style="font-size:large"><br class=""></div></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr"><br class=""></div></div>-- <br class=""><div dir="ltr" class="gmail-m_-3318704790743477738gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><p style="margin-bottom:0cm" align="LEFT" class=""><span class=""><span style="font-family:arial,helvetica,sans-serif" class=""><font size="2" class="">======================================================================</font></span></span></p><p style="margin-bottom:0cm" align="LEFT" class=""><span class=""><span style="font-family:arial,helvetica,sans-serif" class=""><font size="2" class="">Dr Thomas Evangelidis</font></span></span></p><p style="margin-bottom:0cm" align="LEFT" class=""><span style="font-family:arial,helvetica,sans-serif;font-size:small" class="">Research Scientist</span></p><p style="margin-bottom:0cm" align="LEFT" class=""><span style="font-family:arial,helvetica,sans-serif;font-size:small" class=""><a href="https://www.uochb.cz/web/structure/31.html?lang=en" target="_blank" class="">IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences</a></span></p><font size="2" class=""><div class=""><font face="arial, helvetica, sans-serif" class=""><div class="">Prague, Czech Republic</div><div class=""> & </div></font></div><font face="arial, helvetica, sans-serif" class=""><a href="https://www.ceitec.eu/" target="_blank" class="">CEITEC - Central European Institute of Technology</a></font><br class=""><font face="arial, helvetica, sans-serif" class="">Brno, Czech Republic </font></font></div><div class=""><font size="2" class=""><font face="arial, helvetica, sans-serif" class=""><br class=""></font></font></div><div dir="ltr" class=""><p style="margin-bottom:0cm" align="LEFT" class=""><span class=""><span style="font-family:arial,helvetica,sans-serif" class=""><font size="2" class="">email: </font></span></span><a href="mailto:tevang3@gmail.com" style="font-size:small;font-family:arial,helvetica,sans-serif" target="_blank" class="">tevang3@gmail.com</a></p><p style="margin-bottom:0cm" align="LEFT" class=""><span class=""><span style="font-family:arial,helvetica,sans-serif" class=""><font size="2" class="">website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank" class="">https://sites.google.com/site/thomasevangelidishomepage/</a></font></span></span></p><span class=""><br class=""><br class=""></span><div style="margin-bottom:0cm" class="">
<br class="gmail-m_-3318704790743477738webkit-block-placeholder"></div>
</div></div></div></div></div></div></div></div></div></div></div>
<span id="gmail-m_-3318704790743477738cid:f_jtyv3eb40" class=""><1a30_protein.pdb></span><span id="gmail-m_-3318704790743477738cid:f_jtyv3jom1" class=""><1a30_ligand.sdf></span>_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></div></blockquote></div><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><p style="margin-bottom:0cm" align="LEFT" class=""><span style="" class=""><span style="font-family:arial,helvetica,sans-serif" class=""><font size="2" class="">======================================================================</font></span></span></p><p style="margin-bottom:0cm" align="LEFT" class=""><span style="" class=""><span style="font-family:arial,helvetica,sans-serif" class=""><font size="2" class="">Dr Thomas Evangelidis</font></span></span></p><p style="margin-bottom:0cm" align="LEFT" class=""><span style="font-family: arial, helvetica, sans-serif; font-size: small;" class="">Research Scientist</span></p><p style="margin-bottom:0cm" align="LEFT" class=""><span style="font-family: arial, helvetica, sans-serif; font-size: small;" class=""><a href="https://www.uochb.cz/web/structure/31.html?lang=en" target="_blank" class="">IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences</a></span></p><font size="2" class=""><div class=""><font face="arial, helvetica, sans-serif" class=""><div class="">Prague, Czech Republic</div><div class=""> & </div></font></div><font face="arial, helvetica, sans-serif" class=""><a href="https://www.ceitec.eu/" target="_blank" class="">CEITEC - Central European Institute of Technology</a></font><br class=""><font face="arial, helvetica, sans-serif" class="">Brno, Czech Republic </font></font></div><div class=""><font size="2" class=""><font face="arial, helvetica, sans-serif" class=""><br class=""></font></font></div><div dir="ltr" class=""><p style="margin-bottom:0cm" align="LEFT" class=""><span style="" class=""><span style="font-family:arial,helvetica,sans-serif" class=""><font size="2" class="">email: </font></span></span><a href="mailto:tevang3@gmail.com" style="font-size:small;font-family:arial,helvetica,sans-serif" target="_blank" class="">tevang3@gmail.com</a></p><p style="margin-bottom:0cm" align="LEFT" class=""><span style="" class=""><span style="font-family:arial,helvetica,sans-serif" class=""><font size="2" class="">website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank" class="">https://sites.google.com/site/thomasevangelidishomepage/</a></font></span></span></p><span style="" class=""><br class=""><br class=""></span><div style="margin-bottom: 0cm;" class="">
<br class="webkit-block-placeholder"></div>
</div></div></div></div></div></div></div></div></div></div>
_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>