<div dir="ltr">Yes i noticed the _QM modification, I'll run a print_level calculation and lookout by hand<div><br></div><div>Thanks !<br><br>On Tuesday, February 24, 2015 at 11:20:14 PM UTC+1, Teo wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div style="word-wrap:break-word">In QMMM, some atom names have the _QM appended (if I remember correctly), basically their name is modified compared to the classical ones.<div>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><br></div><div><br><div><blockquote type="cite"><div>On 24 Feb 2015, at 17:59, Rolf David <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="j0GHyACvgmMJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">rolf...@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Hi all,<div><br></div>I'm working on a QM/MM calculation<br>I use as coord/topology/FFparamaters a amber12 restart/prmtop.<br><br><div>Everything is nice, except a :<br><br> *** Unknown element for KIND <OP>. This problem can be fixed specifying *** <br> *** properly elements in PDB or specifying a KIND section or getting in *** <br> *** touch with one of the developers! ***<br><br>Of course I have OP Kind in my MM and QM parts (in amber: name OP, type OP, element 8)<br></div><div>(Also another SM Kind only in my MM part, i did the same as OP)</div><div><br></div><div>So, I put a :</div><div><br>&KIND OP<br> ELEMENT O</div><div>&END KIND</div><div> </div><div>In the Subsys section, also I have :</div><div><br></div><div>&KIND O<br></div><div> BASIS_SET 6-31Gxx</div><div> POTENTIAL ALL</div><div>&END KIND</div><div><br></div><div>So everything went smoothly according to plan, and suddenly, I decided to change a part:</div><div><br></div><div><div>&KIND OP<br> ELEMENT O</div><div> BASIS_SET 6-31++Gxx</div><div> POTENTIAL ALL</div><div>&END KIND</div></div><div><br></div><div>and by reading the output all oxygens (O Element) are treated as 6-31Gxx</div><div>I change the order (&Kind O after &Kind OP) no luck.</div><div><br></div><div>How kind/type/element from amber interact with CP2K ?</div><div><br></div><div>I suppose the &KIND in the &SUBSYS are linked to the &QM_KIND in the &QMMM part, only for QMMM atoms ?</div><div><br></div><div>KIND OP exists only amber parm/rst file, so I needed to declare the element -> For the MM part.</div><div><br></div><div>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>By putting &QM_KIND OP, the &KIND OP basis part worked.</div><div><br></div><div>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>in the &QMMM part I have :<br><br></div><div>&MM_KIND OW<br> RADIUS 0.78<br>&END MM_KIND</div><div><br></div><div>It will be applied only to MM atoms, of amber type OW ?</div><div><br></div><div>&KIND correspond to amber name or amber type or both or whatever it feels like it ?</div><div><br></div><div>Confirmations or corrections will be &KINDly appreciated.</div><div><br></div><div>Thanks.</div><div><br></div><div><br></div></div><div><br></div> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="j0GHyACvgmMJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp2k+uns...@googlegroups.<wbr>com</a>.<br> To post to this group, send email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="j0GHyACvgmMJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a>.<br> Visit this group at <a href="http://groups.google.com/group/cp2k" target="_blank" rel="nofollow" onmousedown="this.href='http://groups.google.com/group/cp2k';return true;" onclick="this.href='http://groups.google.com/group/cp2k';return true;">http://groups.google.com/<wbr>group/cp2k</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank" rel="nofollow" onmousedown="this.href='https://groups.google.com/d/optout';return true;" onclick="this.href='https://groups.google.com/d/optout';return true;">https://groups.google.com/d/<wbr>optout</a>.<br> </div></blockquote></div><br></div></div></blockquote></div></div>