<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="">You are correct. The idatmType attribute of atoms was not copied. Explicitly setting idatmTypes isn’t something that happens a lot, so it got overlooked in the copy/combine code. I have fixed that oversight. In tomorrow’s build, idatmTypes that were explicitly set will be copied.<div class=""><br class=""></div><div class="">—Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 5, 2019, at 4:08 AM, 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 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;">I think I found what is wrong. When I do prep() and then split and combine models from the original, the new modes loss their atom types (?). Is this correct? I was led to this conclusion because if I do another prep() to the combined model then I do not get no-GAFF error during initiateAddions().</div><div class="gmail_default" style="font-size: large;"><br class=""></div><div class="gmail_default" style="font-size: large;">best,</div><div class="gmail_default" style="font-size: large;">Thomas</div><div class="gmail_default" style="font-size: large;"> </div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, 2 Apr 2019 at 01:15, 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="">If I do just the commands you provided below on the models you attached earlier 1a30_protein/ligand, I do not get the no-GAFF error you got. I get a different (and later) error that is going to be problematic. Add Ions does not work on multiple models in aggregate — if given multiple models it will add ions to each separately, which is an issue since you’ve separated your receptor and ligand into different models. If you add ions to just the receptor, it could very well place one in the ligand binding pocket. If you combine your ligand and receptor into a single model, that could work but would be more complicated and will probably be a headache. :-(<div class=""><br class=""></div><div class="">Anyway, I’ve attached the script I used that did not get the GAFF error so you can try it yourself on the 1a30 system. You could let me know what additional factors are needed to get the no-GAFF error, assuming that the other Add Ions issue isn’t a showstopper.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></div><div class=""></div></div><div style="word-wrap:break-word" class=""><div class=""></div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Apr 1, 2019, at 3:33 PM, Thomas Evangelidis <<a href="mailto:tevang3@gmail.com" target="_blank" class="">tevang3@gmail.com</a>> wrote:</div><br class="gmail-m_7248682051800945716Apple-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" target="_blank" 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_7248682051800945716gmail-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_7248682051800945716gmail-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_7248682051800945716gmail-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_7248682051800945716gmail-m_-3318704790743477738webkit-block-placeholder"></div>
</div></div></div></div></div></div></div></div></div></div></div>
<span id="gmail-m_7248682051800945716gmail-m_-3318704790743477738cid:f_jtyv3eb40" class=""><1a30_protein.pdb></span><span id="gmail-m_7248682051800945716gmail-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-m_7248682051800945716gmail_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_7248682051800945716webkit-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" 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>
</div></blockquote></div><br class=""></div></body></html>