<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">check that your PDB contains the element field (column 77-78). If you'll provide the element in the PDB, cp2k will not have try to guess the element from the atom name/type.<div><br><div>=> cp2k may rename the types - this could justify why you do not have any HX in your files. There are reasons for renaming - check old posts for the reason.</div><div><br></div><div><br><div><div>On Aug 10, 2013, at 5:08 PM, Geoffrey Wood <<a href="mailto:ge.f...@gmail.com">ge.f...@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Dear Forum,<div><br></div><div>I am reading in an amber topology created by tleap (with the corresponding pdb file created by tleap) but I am getting this error in cp2k (I have no HX's in either of them)? Does any one know what this is about?</div><div><br></div><div>Thanks.</div><div><br></div><div><div> ************************************************************</div><div> *** ERROR in check_subsys_element (MODULE topology_util) ***</div><div> ************************************************************</div><div><br></div><div> *** Unknown element for KIND <HX>. This problem can be fixed specifying ***</div><div> *** properly elements in PDB or specifying a KIND section or getting in ***</div><div> *** touch with one of the developers! ***</div><div><br></div><div> *** Program stopped at line number 1371 of MODULE topology_util ***</div><div><br></div><div> ===== Routine Calling Stack ===== </div><div><br></div><div> 7 connectivity_control_check_element_name</div><div> 6 connectivity_control</div><div> 5 topology_control</div><div> 4 fist_init</div><div> 3 fist_create_force_env</div><div> 2 qmmm_create_force_env</div><div> 1 CP2K</div></div><div><br></div></div><div><br class="webkit-block-placeholder"></div>
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