<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="">If you were using the same input file with the blank residue name, I have no idea how it would have worked before — sorry.<div class=""><br class=""></div><div class="">—Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 1, 2019, at 10:10 PM, 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="">Thank you Sir.. Your suggestion worked perfectly.. There was no problem in minimizing the structure once I assigned a residue name as per your suggestion.<br class=""><br class="">However I had one query, I was able to minimize the same structure earlier without any intermediate step.. But recently this problem of ANTECHAMBER failure popped up. How can I justify this computational anomaly? Please note that neither have I changed my computational system, nor have I uninstalled/reinstalled UCSF Chimera in this period. How could it be so that a structure that could be minimized earlier was creating trouble to minimize recently (until sorted out as per your suggestion).<br class=""><br class="">I will be highly grateful if you can kindly give me some probable reason to justify this anomaly,<br class=""><br class="">Thank you again for your sincere help and prompt support,<div class=""><br class=""></div><div class="">With best regards,<div class=""><br clear="all" class=""><div class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><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 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></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div><br class=""></div></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Oct 2, 2019 at 3:13 AM 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="overflow-wrap: break-word;" class="">Hi Prabuddha,<div class=""><span style="white-space:pre-wrap" class=""> </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 style="white-space:pre-wrap" class=""> </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="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;" class=""><span style="white-space:pre-wrap" class=""><br class=""> </span>Eric Pettersen</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;" class=""><span style="white-space:pre-wrap" class=""> </span>UCSF Computer Graphics Lab</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;" class=""><br class=""></div></div><div class=""><blockquote type="cite" class=""><div class="">On Oct 1, 2019, at 11:43 AM, Prabuddha Bhattacharya <<a href="mailto:b.prabuddha3@gmail.com" target="_blank" class="">b.prabuddha3@gmail.com</a>> wrote:</div><br class=""><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=""><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="gmail-m_3608273509325495523cid:f_k186maf20" class=""><sulfonamide-pdb.pdb></span><span id="gmail-m_3608273509325495523cid:f_k186ndg01" class=""><energy minimization problem.docx></span><span id="gmail-m_3608273509325495523cid:f_k186w2hs2" class=""><vb.pdb></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 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>