<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">In QMMM, some atom names have the _QM appended (if I remember correctly), basically their name is modified compared to the classical ones.<div class="">To find it out the correct names, run enabling the proper print section (or alternatively a print_level medium should do that work for you).</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 24 Feb 2015, at 17:59, Rolf David <<a href="mailto:rolf.d...@gmail.com" class="">rolf.d...@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi all,<div class=""><br class=""></div>I'm working on a QM/MM calculation<br class="">I use as coord/topology/FFparamaters a amber12 restart/prmtop.<br class=""><br class=""><div class="">Everything is nice, except a :<br class=""><br class=""> *** Unknown element for KIND <OP>. This problem can be fixed specifying *** <br class=""> *** properly elements in PDB or specifying a KIND section or getting in *** <br class=""> *** touch with one of the developers! ***<br class=""><br class="">Of course I have OP Kind in my MM and QM parts (in amber: name OP, type OP, element 8)<br class=""></div><div class="">(Also another SM Kind only in my MM part, i did the same as OP)</div><div class=""><br class=""></div><div class="">So, I put a :</div><div class=""><br class="">&KIND OP<br class=""> ELEMENT O</div><div class="">&END KIND</div><div class=""> </div><div class="">In the Subsys section, also I have :</div><div class=""><br class=""></div><div class="">&KIND O<br class=""></div><div class=""> BASIS_SET 6-31Gxx</div><div class=""> POTENTIAL ALL</div><div class="">&END KIND</div><div class=""><br class=""></div><div class="">So everything went smoothly according to plan, and suddenly, I decided to change a part:</div><div class=""><br class=""></div><div class=""><div class="">&KIND OP<br class=""> ELEMENT O</div><div class=""> BASIS_SET 6-31++Gxx</div><div class=""> POTENTIAL ALL</div><div class="">&END KIND</div></div><div class=""><br class=""></div><div class="">and by reading the output all oxygens (O Element) are treated as 6-31Gxx</div><div class="">I change the order (&Kind O after &Kind OP) no luck.</div><div class=""><br class=""></div><div class="">How kind/type/element from amber interact with CP2K ?</div><div class=""><br class=""></div><div class="">I suppose the &KIND in the &SUBSYS are linked to the &QM_KIND in the &QMMM part, only for QMMM atoms ?</div><div class=""><br class=""></div><div class="">KIND OP exists only amber parm/rst file, so I needed to declare the element -> For the MM part.</div><div class=""><br class=""></div><div class="">But since in my &QMMM part, I only have &QM_KIND O for all my oxygens, putting a basis/potential for OP has no effect so I have to declare a &QM_KIND OP.</div><div class="">By putting &QM_KIND OP, the &KIND OP basis part worked.</div><div class=""><br class=""></div><div class="">What about atom type (amber type, amber name, so complicated...) like for TIP3P water, O is the name, and OW is the type</div><div class="">in the &QMMM part I have :<br class=""><br class=""></div><div class="">&MM_KIND OW<br class=""> RADIUS 0.78<br class="">&END MM_KIND</div><div class=""><br class=""></div><div class="">It will be applied only to MM atoms, of amber type OW ?</div><div class=""><br class=""></div><div class="">&KIND correspond to amber name or amber type or both or whatever it feels like it ?</div><div class=""><br class=""></div><div class="">Confirmations or corrections will be &KINDly appreciated.</div><div class=""><br class=""></div><div class="">Thanks.</div><div class=""><br class=""></div><div class=""><br class=""></div></div><div class=""><br class="webkit-block-placeholder"></div>
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