<div dir="ltr"><div><div>Dear Ghazaleh,</div><div><br></div><div>Thank you very much for your helpful answer.</div><div><br></div><div>Your suggestion seems to work indeed if in addition I change the element type to one of the known elements. (Also, I found that in the attached CHARMM paramter input file the DIHEDRALS keyword was incorrect.)</div><div><br></div><div>Best wishes,</div><div>Christoph</div><div><br></div></div><br><br>On Tuesday, June 27, 2017 at 6:17:57 AM UTC-4, Ghazaleh Zm wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Christoph<div><br></div><div>I‌ had similar problem as yours recently. </div><div>In your version 1 input file, you defined Kind A1, Kind A2, Kind A3, while in your PSF file these are atom names and the atom types are A, A, and B (the next tab). </div><div>Therefore you should define Kind A and Kind B in the input file. <br><br>I hope it helps you. </div><div><br></div><div>Ghazaleh </div><div><br></div><div>On Monday, June 26, 2017 at 9:04:26 PM UTC+2, Christoph wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear CP2K users,<div><br></div><div>I would simulate on the MM level an artificial test system with CP2K (artificial refering here to the atom types), using CHARMM topology/parameter files.</div><div><br></div><div>As a minimal example, I have prepared a geometry optimization for a 3-atomic molecule, which I fail to get working for MM only simulations. The input files for two versions, 1 and 2, are attached.</div><div><br></div><div>When running version 1 I get:</div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><font size="1"><br></font></div><div><div><font size="1"> *****************************<wbr>******************************<wbr>********************</font></div></div><div><div><font size="1"> * ___ *</font></div></div><div><div><font size="1"> * / \ *</font></div></div><div><div><font size="1"> * [ABORT] Unknown element for KIND <A>. This problem can be fixed specifying *</font></div></div><div><div><font size="1"> * \___/ properly elements in PDB or specifying a KIND section or getting in *</font></div></div><div><div><font size="1"> * | touch with one of the developers! *</font></div></div><div><div><font size="1"> * O/| *</font></div></div><div><div><font size="1"> * /| | *</font></div></div><div><div><font size="1"> * / \ topology_util.F:1271 *</font></div></div><div><div><font size="1"> *****************************<wbr>******************************<wbr>********************</font></div></div><div><div><font size="1"><br></font></div></div><div><div><font size="1"><br></font></div></div><div><div><font size="1"> ===== Routine Calling Stack ===== </font></div></div><div><div><font size="1"><br></font></div></div><div><div><font size="1"> 6 connectivity_control_check_<wbr>element_name</font></div></div><div><div><font size="1"> 5 connectivity_control</font></div></div><div><div><font size="1"> 4 topology_control</font></div></div><div><div><font size="1"> 3 fist_init</font></div></div><div><div><font size="1"> 2 fist_create_force_env</font></div></div><div><div><font size="1"> 1 CP2K</font></div></div><div><div><font size="1"><br></font></div></div><div><div><font size="1">Program received signal SIGABRT: Process abort signal.</font></div></div><div><div><font size="1"><br></font></div></div><div><div><font size="1">Backtrace for this error:</font></div></div><div><div><font size="1">#0 0x23458CD in _gfortrani_backtrace at backtrace.c:258</font></div></div><div><div><font size="1">#1 0x2320A20 in _gfortrani_backtrace_handler at compile_options.c:129</font></div></div><div><div><font size="1">#2 0x42DE5F in _L_unlock_13 at funlockfile.c:?</font></div></div><div><div><font size="1">#3 0x42DD2B in raise at pt-raise.c:37</font></div></div><div><div><font size="1">#4 0x23BF037 in abort at abort.c:78</font></div></div><div><div><font size="1">#5 0x1E20288 in __message_passing_MOD_mp_abort at message_passing.F:1034</font></div></div><div><div><font size="1">#6 0x1E74B87 in __base_hooks_MOD_cp_abort at base_hooks.F:68</font></div></div><div><div><font size="1">#7 0xF33EE6 in __topology_util_MOD_check_<wbr>subsys_element at topology_util.F:1275 (discriminator 15)</font></div></div><div><div><font size="1">#8 0xC2AE9A in __topology_MOD_connectivity_<wbr>control at topology.F:355</font></div></div><div><div><font size="1">#9 0xC2BBEC in __topology_MOD_topology_<wbr>control at topology.F:187</font></div></div><div><div><font size="1">#10 0x7B561B in __cp_subsys_methods_MOD_cp_<wbr>subsys_create at cp_subsys_methods.F:152</font></div></div><div><div><font size="1">#11 0x141C867 in __fist_environment_MOD_fist_<wbr>init at fist_environment.F:161</font></div></div><div><div><font size="1">#12 0x137345F in __fist_main_MOD_fist_create_<wbr>force_env at fist_main.F:97</font></div></div><div><div><font size="1">#13 0xBA17C1 in __f77_interface_MOD_create_<wbr>force_env at f77_interface.F:752</font></div></div><div><div><font size="1">#14 0x437116 in __cp2k_runs_MOD_cp2k_run at cp2k_runs.F:276</font></div></div><div><div><font size="1">#15 0x43AA9C in __cp2k_runs_MOD_run_input at cp2k_runs.F:1099</font></div></div><div><div><font size="1">#16 0x4301DE in MAIN__ at cp2k.F:281</font></div></div></blockquote><div><br></div><div><br></div><div>I guess one cannot specify new element types in CP2K via the input files only. In version 2 of my example files the atom type is changed to "C" (both in the PDB and the CP2K KIND input files), which should be known by CP2K. However, I get with when running version 2:</div><div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div><font size="1"> *****************************<wbr>******************************<wbr>********************</font></div></div><div><div><font size="1"> * ___ *</font></div></div><div><div><font size="1"> * / \ *</font></div></div><div><div><font size="1"> * [ABORT] *</font></div></div><div><div><font size="1"> * \___/ A string type object was expected, found end of line, File: *</font></div></div><div><div><font size="1"> * | '../system1.prm', Line: 13, Column: 6 *</font></div></div><div><div><font size="1"> * O/| *</font></div></div><div><div><font size="1"> * /| | *</font></div></div><div><div><font size="1"> * / \ input/cp_parser_methods.F:<wbr>1253 *</font></div></div><div><div><font size="1"> *****************************<wbr>******************************<wbr>********************</font></div></div><div><div><font size="1"><br></font></div></div><div><div><font size="1"><br></font></div></div><div><div><font size="1"> ===== Routine Calling Stack ===== </font></div></div><div><div><font size="1"><br></font></div></div><div><div><font size="1"> 5 read_force_field_charmm</font></div></div><div><div><font size="1"> 4 force_field_control</font></div></div><div><div><font size="1"> 3 fist_init</font></div></div><div><div><font size="1"> 2 fist_create_force_env</font></div></div><div><div><font size="1"> 1 CP2K</font></div></div><div><div><font size="1"><br></font></div></div><div><div><font size="1">Program received signal SIGABRT: Process abort signal.</font></div></div><div><div><font size="1"><br></font></div></div><div><div><font size="1">Backtrace for this error:</font></div></div><div><div><font size="1">#0 0x23458CD in _gfortrani_backtrace at backtrace.c:258</font></div></div><div><div><font size="1">#1 0x2320A20 in _gfortrani_backtrace_handler at compile_options.c:129</font></div></div><div><div><font size="1">#2 0x42DE5F in _L_unlock_13 at funlockfile.c:?</font></div></div><div><div><font size="1">#3 0x42DD2B in raise at pt-raise.c:37</font></div></div><div><div><font size="1">#4 0x23BF037 in abort at abort.c:78</font></div></div><div><div><font size="1">#5 0x1E20288 in __message_passing_MOD_mp_abort at message_passing.F:1034</font></div></div><div><div><font size="1">#6 0x1E74B87 in __base_hooks_MOD_cp_abort at base_hooks.F:68</font></div></div><div><div><font size="1">#7 0x19C149C in __cp_parser_methods_MOD_<wbr>parser_get_string at cp_parser_methods.F:1255 (discriminator 2)</font></div></div><div><div><font size="1">#8 0x15789FF in __force_fields_ext_MOD_read_<wbr>force_field_charmm at force_fields_ext.F:434</font></div></div><div><div><font size="1">#9 0x141D28D in __force_fields_MOD_force_<wbr>field_control at force_fields.F:158</font></div></div><div><div><font size="1">#10 0x141C90C in __fist_environment_MOD_fist_<wbr>init at fist_environment.F:169</font></div></div><div><div><font size="1">#11 0x137345F in __fist_main_MOD_fist_create_<wbr>force_env at fist_main.F:97</font></div></div><div><div><font size="1">#12 0xBA17C1 in __f77_interface_MOD_create_<wbr>force_env at f77_interface.F:752</font></div></div><div><div><font size="1">#13 0x437116 in __cp2k_runs_MOD_cp2k_run at cp2k_runs.F:276</font></div></div><div><div><font size="1">#14 0x43AA9C in __cp2k_runs_MOD_run_input at cp2k_runs.F:1099</font></div></div><div><div><font size="1">#15 0x4301DE in MAIN__ at cp2k.F:281</font></div></div><div><div><font size="1">/home/jadzia/Dropbox/Software/<wbr>installed/bin/cp2k: line 5: 2732 Aborted ${script_dir}/cp2k.ssmp $@</font></div></div></blockquote><div><br></div><div><br></div><div>If possible I would like to get this working with them CHARMM files rather than with CP2K keywords. I know that there are other programs which are specialized on MM simulations, but I want to use CP2K due to some special features it has. </div><div><br></div><div>Looking forward to your comments.</div><div><br></div><div>Best wishes,</div><div>Christoph</div></div></blockquote></div></div></blockquote></div>