<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi,<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>What created these PDB files? I only looked briefly at the first one (top-2-2242.pdb), but for instance residue 66 in chain A has two copies of every atom (at different coordinates) except for the C and the O. I’m guessing the the original PDB file had alternate-location indicators to differentiate between the atoms, but that those indicators were dropped by whatever program wrote this version of the file. At any rate, Chimera will not be able to perform minimization on such a file. So the first thing you need to do is fix the program that wrote this file so that it outputs a legal PDB file.<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Once you’ve done that, then I can help you with any further problems you have. You should report errors to <a href="mailto:chimera-bugs@cgl.ucsf.edu" class="">chimera-bugs@cgl.ucsf.edu</a> rather than chimera-users. Besides regular email, you can also use Help->Report A Bug in the Chimera menus to do so.</div><div class=""><br class=""></div><div class="">--Eric<br class=""><br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab<div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Aug 6, 2017, at 5:01 AM, Ch Bilal <<a href="mailto:ch.bilal321@outlook.com" class="">ch.bilal321@outlook.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" style="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; -webkit-text-stroke-width: 0px; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Respected Sir/Madam.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Its Bilal here and i m doing research on a protein "rstA". I am UCSF Chimera user and i am facing an error while energy minimization i got a pop up windows with this error "No MMKT name of atom "HN1" in standard residue "LYS", please help me out i am attaching my complexes with this mail as well please find the attachment.</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Thank you!<br class=""></div></div><span id="cid:C8FA7C4F-DBC7-4218-A382-FCB6B7775F99@cgl.ucsf.edu"><top-2-2242.pdb></span><span id="cid:8A0E1448-B43F-4092-A4C7-5D04F7189ED2@cgl.ucsf.edu"><top-3-1610.pdb></span><span id="cid:5D23B241-5C6C-4617-B699-D21C2FC346E8@cgl.ucsf.edu"><top-4-530.pdb></span><span 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; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br 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; -webkit-text-stroke-width: 0px;" class=""><span 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; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="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;" class="">Chimera-users@cgl.ucsf.edu</a><br 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; -webkit-text-stroke-width: 0px;" class=""><span 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; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="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;" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br class=""></div></div></body></html>