<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 Selva,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Your structure minimizes without error for me. Instead of going back and forth on the mailing list, can you use Help→Report A Bug in Chimera to submit a bug report? That will provide me with a lot information, such as the version of Chimera you're using, what platform you're on, <i class="">etc</i>. without me asking a bunch of questions or guessing. Thanks!</div><div class=""><br class=""></div><div class="">--Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jan 23, 2023, at 8:29 PM, SELVA BABU SELVAMANI via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Dear Eric,</div><div class=""><br class=""></div><div class="">Here with I am attached the structure I phosphorylated, please kindly help regarding this.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Thank you!</div><div class=""><br class=""></div><div class=""><br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Jan 24, 2023 at 7:01 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 Selva,<div class=""><span style="white-space:pre-wrap" class=""> </span>I am able to carry out minimization without problem on 1G6G, which has a TPO residue. Does your TPO residue and its adjacent residues have all their atoms present? You might have to send me the structure if that's not the problem.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span style="white-space:pre-wrap" class=""> </span>Eric Pettersen</div><div class=""><span style="white-space:pre-wrap" class=""> </span>UCSF Computer Graphics Lab</div></div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Jan 21, 2023, at 4:29 AM, SELVA BABU SELVAMANI via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class=""><div class="">Dear Developers,</div><div class=""><br class=""></div><div class="">I did phosphorylation of amino acid in protein, then I was about to do energy minimization using Chimera MINIMIZE STRUCTURE module, but it is throwing the error ( I mentioned below ).</div><div class=""><br class=""></div><div class="">****************************************************<br class="">Running PARMCHK for PP.pdb<br class="">Using main parameter file parm10.dat modified by heme-iron.frcmod, frcmod.ff14SB, frcmod.ionsjc_tip3p<br class=""><font size="4" class=""><b class="">Chimera/MMTK cannot minimize structure, probably because there is no parameter for ''No parameters for bond Atom 0.TPO_144__0_0_1_145.N (atom type n) - Atom 0.GLN_143__0_0_1_144.peptide.C (atom type C)''</b></font></div><div class=""><font size="4" class=""><b class="">********************************************</b></font></div><div class=""><br class=""></div><div class=""><font size="4" class=""><b class="">Please help me to sort out the issue.</b></font></div><div class=""><br class=""></div><div class=""><font size="4" class="">I also tried to do phosphorylate using Chimera, even that structure also getting the same error while doing energy minimization.</font><br class=""></div><div class="">-- <br class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><span style="color:rgb(0,0,255)" class=""><span style="background-color:rgb(255,255,255)" class=""><b class="">Have a nice day,</b></span></span></div><div dir="ltr" class="">Thanks & Regards,<div class=""><font color="#ff0000" class=""><b class=""><font size="4" class="">SELVA BABU S</font></b></font></div>M.Sc Scholar (Bioinformatics)</div><div dir="ltr" class=""><div class=""><b class="">TNAU, Coimbatore<br class=""></b></div></div></div></div></div></div>
_______________________________________________<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="https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users" target="_blank" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></div></blockquote></div><br clear="all" class=""><br class="">-- <br class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><div class=""><span style="color:rgb(0,0,255)" class=""><span style="background-color:rgb(255,255,255)" class=""><b class="">Have a nice day,</b></span></span></div><div dir="ltr" class="">Thanks & Regards,<div class=""><font color="#ff0000" class=""><b class=""><font size="4" class="">SELVA BABU S</font></b></font></div>M.Sc Scholar (Bioinformatics)</div><div dir="ltr" class=""><div class=""><b class="">TNAU, Coimbatore<br class=""></b></div></div></div></div>
<span id="cid:f_ld9qnf2y0"><phosphorylated_protein.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="https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>