<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="">It turns out that without a cofactor stabilizing the position of the iron, the ff14SB force field parameters are such that the iron will minimize to be somewhat non-planar with the porphyrin ring. For instance if I take the 2j0p structure and delete everything but the heme and then run 1000 steps of steepest descent, the iron moves out of the plane of the ring.<div class=""><br class=""></div><div class="">The OPLS force field has explicit parameters for maintaining the ring planarity of the iron, but that is beyond the scope of Chimera. You would have to run Amber of some other package yourself.</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 15, 2019, at 8:44 PM, <a href="mailto:sara20@mail.ustc.edu.cn" class="">sara20@mail.ustc.edu.cn</a> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Hi Eric</div><div style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Thanks for your suggestions. I tried the mentioned steps but still facing the same issue (see attached file). I forgot to mention that I am minimizing the modelled structure, maybe that's why it's creating this problem. In modelling I modelled the structure with heme and also with out heme (and later on pasted the heme coordinates from template to model structure). I minimized both structures and ended up with the same problem. I am not sure where am I making mistake. I'd be grateful if you could guide me more.</div><div style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Regards</div><div style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Sara</div><br style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><blockquote class="ReferenceQuote" name="replyContent" style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none; padding-left: 5px; margin-left: 5px; border-left-width: 2px; border-left-style: solid; border-left-color: rgb(182, 182, 182); margin-right: 0px;">-----Original Messages-----<br class=""><b class="">From:</b><span id="rc_from" class="">"Eric Pettersen" <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>></span><br class=""><b class="">Sent Time:</b><span id="rc_senttime" class="">2019-07-16 06:55:59 (Tuesday)</span><br class=""><b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:sara20@mail.ustc.edu.cn" class="">sara20@mail.ustc.edu.cn</a><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span>"<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span>BB" <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] energy minimization<br class=""><br class="">Hi Sara,<div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>There are a couple of problems here. One is that the heme coordinates / bond lengths aren’t very good, so Chimera’s estimates for the atom types is wrong for some of the atoms. The other problem is that because the iron is displaced out of the porphyrin ring, addh is adding hydrogens to the inside of the ring that would normally be prevented by the presence of the iron. Those hydrogens repel the iron of course.</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>So, to correct things, you need to:</div><div class=""><br class=""></div><div class="">1) Delete all hydrogens</div><div class="">2) Correct the atom types</div><div class="">3) Add the hydrogens back</div><div class="">4) Delete inward-facing porphyrin-ring hydrogens</div><div class="">5) Add charges</div><div class="">6) Minimize</div><div class=""><br class=""></div><div class="">The commands (Favorites→Command Line) corresponding to those steps are:</div><div class=""><br class=""></div><div class="">1) “del H”</div><div class="">2) “defattr /path/to/heme.defattr raise false” (I have attached the heme.defattr file) </div><div class="">3) “addh”</div><div class="">4) “del :hem@hd”</div><div class="">5) “addch” (this will take awhile with AM1-BCC charges)</div><div class="">6) Minimize however you were doing it before.</div><div class=""><br class=""></div><div class="">I have also attached a session with all the above steps performed. The iron is not yet planar with the ring, but additional minimization will undoubtedly get it there.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></div><div class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div><div class=""></div></blockquote><span id="cid:05EC61C4-FCB4-41ED-BB0D-02CE1902ABF8@cgl.ucsf.edu"><minnewRefined_model7.pdb></span><span style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none; 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="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-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; -webkit-text-stroke-width: 0px; text-decoration: none; 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></body></html>