<div dir="ltr"><div>Dear Rizwan,</div><div><br></div><div>Thank you, such a silly mistake. I can continue but run into other errors which so far I am able to deal with.</div><div>However I will be back soon with new questions, I'm sure :).</div><div><br></div><div>Best wishes,</div><div>Dawid<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2018-05-31 1:30 GMT+02:00 Rizwan Nabi <span dir="ltr"><<a href="mailto:rizwan...@gmail.com" target="_blank">rizwan...@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto">Dear David <div dir="auto">You have to mention basis sets for O atoms as well in the &KIND section of input </div></div><div class="HOEnZb"><div class="h5"><br><div class="gmail_quote"><div dir="ltr">On Thu, 31 May 2018, 00:48 'Dawid das' via cp2k, <<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Dear CP2K Users,</div><div><br></div><div>I am completely new to CP2K and I would like to perform QM/MM molecular dynamics simulation of protein <br></div><div>solvated in a box of water with counterions (system is neutral).</div><div><br></div><div>I would like to do it at the B3LYP/GPAW or B3LYP/GPW level of theory for QM subsystem and CHARMM22 <br></div><div>force field for classical part. I use link atoms approach, PBC (at least for electrostatics in classical part, <br></div><div>I don't know how about the QM part yet) and electrostatic embedding. I think these are the most important <br></div><div>points of what I want to do.</div><div><br></div><div>I went through exemplary inputs for QM/MM MD simulations I could find on this group and on CP2K website</div><div>and there is one thing however I cannot overcome but I think I know the source of issue.</div><div><br></div><div>My protein is a fluorescent protein and I have definition of non-standard atom types in my CHARMM force <br></div><div>field.</div><div>At the end of the log I get following error:</div><div><br></div><div><span style="font-family:courier new,monospace"> *****************************<wbr>***********************<br> *** ERROR in read_qs_kind (MODULE qs_kind_types) ***<br> *****************************<wbr>***********************<br><br> *** No &KIND section was possible to associate to the atomic kind <O>. ***<br> *** The KIND section were also scanned for the corresponding element <O> ***<br> *** and for the DEFAULT section but no match was found. Check your input ***<br> *** file! <wbr> <wbr> ***<br><br> *** Program stopped at line number 1840 of MODULE qs_kind_types ***</span><br></div><div><br></div><div>I don't really know how to proceed further...</div><div>I guess CP2K cannot recognize correctly MO3, MOH, MN3, etc. types as oxygen, nitrogen, etc.</div><div>I tried to play with &KIND section but I'm not really sure how to make it to make sense.<br></div><div>I attach my input files and I will be grateful for any explanations. The QM subsystem is for <br></div><div>now very small as I just want to start off a simulation to check whether it works or not.</div><div><br></div><div>Best wishes,</div><div>Dawid Grabarek<br></div></div>
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