<div dir="ltr">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><br>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><br>I will be highly grateful if you can kindly give me some probable reason to justify this anomaly,<br><br>Thank you again for your sincere help and prompt support,<div><br></div><div>With best regards,<div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><font face="garamond, serif" size="2"><b>Prabuddha Bhattacharya </b></font></div><div><font face="garamond, serif" size="2"><b>Assistant Professor</b></font></div><div><font face="garamond, serif" size="2"><b>Adamas University</b></font></div><div><font face="garamond, serif"><b>Kolkata 700126</b></font></div><div><font face="garamond, serif"><b>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></div></div></div><br><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">pett@cgl.ucsf.edu</a>> wrote:<br></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;">Hi Prabuddha,<div><span style="white-space:pre-wrap"> </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><br></div><div><span style="white-space:pre-wrap"> </span>setattr r type UNL #0</div><div><br></div><div>Then both Gasteiger and AM1-BCC minimizations will work.</div><div><br></div><div>—Eric<br><div>
<div style="color:rgb(0,0,0);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"><span style="white-space:pre-wrap"><br> </span>Eric Pettersen</div><div style="color:rgb(0,0,0);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"><span style="white-space:pre-wrap"> </span>UCSF Computer Graphics Lab</div><div style="color:rgb(0,0,0);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"><br></div></div><div><blockquote type="cite"><div>On Oct 1, 2019, at 11:43 AM, Prabuddha Bhattacharya <<a href="mailto:b.prabuddha3@gmail.com" target="_blank">b.prabuddha3@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Dear Chimera,<div><br></div><div>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><br>Upon trying out with "AM1-BCC"
(for other non-standard residues), I am getting an altered compound so that cannot be perhaps tried.<br><br>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><br>I will be highly grateful if you can help me in sorting out the problem.<br><br>Thanks in advance,<br><br>Best Regards,</div><div><br clear="all"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><font face="garamond, serif" size="2"><b>Prabuddha Bhattacharya </b></font></div><div><font face="garamond, serif" size="2"><b>Assistant Professor</b></font></div><div><font face="garamond, serif" size="2"><b>Adamas University</b></font></div><div><font face="garamond, serif"><b>Kolkata 700126</b></font></div><div><font face="garamond, serif"><b>India</b></font></div><div><br></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"><sulfonamide-pdb.pdb></span><span id="gmail-m_3608273509325495523cid:f_k186ndg01"><energy minimization problem.docx></span><span id="gmail-m_3608273509325495523cid:f_k186w2hs2"><vb.pdb></span>_______________________________________________<br>Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a><br>Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></blockquote></div><br></div></div></blockquote></div>