<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 Prabuddha,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The underlying AmberTools programs that Chimera is calling to perform the atom typing and minimization don’t work properly if the residue name is blank. If your sulfonamide is open as model #0, do this command (Favorites→Command Line) before minimizing in order to assign a residue name of “UNL”:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>setattr r type UNL #0</div><div class=""><br class=""></div><div class="">Then both Gasteiger and AM1-BCC minimizations will work.</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div class="">
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"><br class="Apple-interchange-newline"> </span>Eric Pettersen</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div></div><div><blockquote type="cite" class=""><div class="">On Oct 1, 2019, at 11:43 AM, Prabuddha Bhattacharya <<a href="mailto:b.prabuddha3@gmail.com" class="">b.prabuddha3@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Dear Chimera,<div class=""><br class=""></div><div class="">I have been facing a problem recently while using UCSF Chimera. After opening the structure of ligands in the chimera window as .pdb file, when ever I am trying to minimize the energy (Tools-->Structure Editing-->Minimize Structure) of that ligand in (which is in .pdb form), I am getting the following error message: "Failure running ANTECHAMBER for residue". I am using "AMBER ff14SB" (for standard residues) and "Gasteiger" (for other non-standard residues). <br class=""><br class="">Upon trying out with "AM1-BCC"
(for other non-standard residues), I am getting an altered compound so that cannot be perhaps tried.<br class=""><br class="">Kindly find attached the .pdb files for the ligands I am trying to minimize the energy, and a word file containing the screen shots of the step-by-step messages leading to the error message that I am getting.<br class=""><br class="">I will be highly grateful if you can help me in sorting out the problem.<br class=""><br class="">Thanks in advance,<br class=""><br class="">Best Regards,</div><div class=""><br clear="all" class=""><div class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><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 dir="ltr" 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 dir="ltr" class=""><font face="garamond, serif" size="2" class=""><b class="">Prabuddha Bhattacharya </b></font></div><div class=""><font face="garamond, serif" size="2" class=""><b class="">Assistant Professor</b></font></div><div class=""><font face="garamond, serif" size="2" class=""><b class="">Adamas University</b></font></div><div class=""><font face="garamond, serif" class=""><b class="">Kolkata 700126</b></font></div><div class=""><font face="garamond, serif" class=""><b class="">India</b></font></div><div class=""><br class=""></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<span id="cid:f_k186maf20"><sulfonamide-pdb.pdb></span><span id="cid:f_k186ndg01"><energy minimization problem.docx></span><span id="cid:f_k186w2hs2"><vb.pdb></span>_______________________________________________<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>