<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255); text-decoration-thickness: initial;" class=""><font face="Roboto, RobotoDraft, Helvetica, Arial, sans-serif" class=""><div style="caret-color: rgba(0, 0, 0, 0.87); color: rgba(0, 0, 0, 0.87); font-size: 14px;" class=""></div></font></div><div><br class=""><blockquote type="cite" class=""><div class="">On 3 Mar 2021, at 20:58, Amami Haruka <<a href="mailto:amami...@gmail.com" class="">amami...@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">Ok, I solved the problem.<div class=""><div class="">If your input file has an unusual atom mapping. For example, a proton in your ligand has atom name HX.</div><div class="">cp2k could only recognise this mapping from HX to H, if both the topology file and coordinate file are provided.</div><div class=""><br class=""></div><div class="">So you would need</div><div class=""><br class=""></div><div class=""><div class=""> &TOPOLOGY</div><div class=""> CONN_FILE_FORMAT AMBER</div><div class=""> CONN_FILE_NAME MM.prmtop</div><div class=""> COORD_FILE_NAME npt.pdb</div><div class=""> COORD_FILE_FORMAT PDB</div><div class=""> &END TOPOLOGY</div><div class=""><br class=""></div><div class="">and this won't work.</div><div class=""><br class=""></div><div class=""><div class=""> &TOPOLOGY</div><div class=""> CONN_FILE_FORMAT AMBER</div><div class=""> CONN_FILE_NAME MM.prmtop</div><div class=""> &END TOPOLOGY</div></div><div class=""><br class=""></div><div class="">Given that the amber topology contains this mapping information, I think it would be more useful if the cp2k could read this mapping information when only CONN_FILE is provided.</div><div class="">In cp2k-8.1/src/topology_util.F, SUBROUTINE check_subsys_element(element_in, atom_name_in, element_out, subsys_section, use_mm_map_first) doesn't seems to do this.</div><div class=""><br class=""></div></div></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, 3 March 2021 at 15:45:41 UTC Amami Haruka wrote:<br class=""></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div style="word-wrap:break-word;line-break:after-white-space" class="">Sorry, there seems to be a problem with attaching files.<div class=""></div></div></blockquote></div><div class=""><br class="webkit-block-placeholder"></div>
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