<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="">Hi Thomas,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera does its own charge estimation, based on the atom types it’s computed for the ligand. The routine is called estimateNetCharge and it’s found in the AddCharge module in your Chimera distribution. It’s a fairly complicated routine.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Specifically the file you will find estimateNetCharge in is:</div><div class=""><br class=""></div><div class="">Mac:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera.app/Contents/Resources/share/AddCharge/__init__.py</div><div class=""><br class=""></div><div class="">Linux/Windows:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><Chimera install location>/share/AddCharge/__init__.py</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></div><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><br class=""><blockquote type="cite" class=""><div class="">On Aug 21, 2019, at 9:00 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;">Greetings,<br clear="all" class=""></div><div class="gmail_default" style="font-size: large;"><br class=""></div><div class="gmail_default" style="font-size: large;">How does Chimera guess the net charge of a ligand when prompted to select the charge type (AM1-bcc or Gasteiger)? I am doing high throughput protein-ligand MD simulations and would like to know which open source library Chimera uses for this task.</div><div class="gmail_default" style="font-size: large;"><br class=""></div><div class="gmail_default" style="font-size: large;">Thanks in advance.</div><div class="gmail_default" style="font-size: large;">Thomas </div><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" 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><span style="font-family: arial, helvetica, sans-serif;" class="">Prague, Czech Republic</span></p><font size="2" class=""><div class=""><font face="arial, helvetica, sans-serif" class=""><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><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>, Twitter: <a href="https://twitter.com/tevangelidis" target="_blank" class="">tevangelidis</a>, LinkedIn: <a href="https://www.linkedin.com/in/thomas-evangelidis-495b45125/" target="_blank" class="">Thomas Evangelidis</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=""><br class=""></span><div style="margin-bottom: 0cm;" class="">
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