<div dir="ltr"><div dir="ltr"><div dir="ltr"><div class="gmail_default" style="font-size:large;color:rgb(0,0,0)">Hi Eric,</div><div class="gmail_default" style="font-size:large;color:rgb(0,0,0)"><br></div><div class="gmail_default" style="font-size:large;color:rgb(0,0,0)">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;color:rgb(0,0,0)"><br></div><div class="gmail_default" style="font-size:large;color:rgb(0,0,0)"><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><br></div></div><div class="gmail_default" style="font-size:large;color:rgb(0,0,0)"><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr"><br></div></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>
<p style="margin-bottom:0cm" align="LEFT"><span style="color:rgb(0,0,0)"><span style="font-family:arial,helvetica,sans-serif"><font size="2">======================================================================</font></span></span></p>
<p style="margin-bottom:0cm" align="LEFT"><span style="color:rgb(0,0,0)"><span style="font-family:arial,helvetica,sans-serif"><font size="2">Dr Thomas Evangelidis</font></span></span></p><p style="margin-bottom:0cm" align="LEFT"><span style="color:rgb(0,0,0);font-family:arial,helvetica,sans-serif;font-size:small">Research Scientist</span></p><p style="margin-bottom:0cm" align="LEFT"><span style="color:rgb(0,0,0);font-family:arial,helvetica,sans-serif;font-size:small"><a href="https://www.uochb.cz/web/structure/31.html?lang=en" target="_blank">IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences</a></span></p><font size="2"><div><font color="#000000" face="arial, helvetica, sans-serif"><div>Prague, Czech Republic</div><div> & </div></font></div><font color="#000000" face="arial, helvetica, sans-serif"><a href="https://www.ceitec.eu/" target="_blank">CEITEC - Central European Institute of Technology</a></font><br><font color="#000000" face="arial, helvetica, sans-serif">Brno, Czech Republic </font></font></div><div><font size="2"><font color="#000000" face="arial, helvetica, sans-serif"><br></font></font></div><div dir="ltr"><p style="margin-bottom:0cm" align="LEFT"><span style="color:rgb(0,0,0)"><span style="font-family:arial,helvetica,sans-serif"><font size="2">email: </font></span></span><a href="mailto:tevang3@gmail.com" style="font-size:small;font-family:arial,helvetica,sans-serif" target="_blank">tevang3@gmail.com</a></p><p style="margin-bottom:0cm" align="LEFT"><span style="color:rgb(0,0,0)"><span style="font-family:arial,helvetica,sans-serif"><font size="2">website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></font></span></span></p><span style="color:rgb(0,0,0)"><br><br></span><p style="margin-bottom:0cm" align="LEFT">
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