<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">double check your PSF or PDB.. the error is self-esplicative : there must be two or more molecules that have the same name but have different atom sequence..<div class=""><br class=""></div><div class="">the fact your PSF or PDB may work with other codes means only that such codes are not performing tight checks.</div><div class=""><br class=""></div><div class="">Teo</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 11 Feb 2015, at 18:51, cjor <<a href="mailto:chri...@gmail.com" class="">chri...@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello, <div class="">I'm trying to run a QMMM simulation with CP2K based on a CHARMM FF MD simulation.</div><div class=""><br class=""></div><div class="">I first tried to run MM to see it works, but I get the following error:</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">"</div><div class=""><div class=""> CP2K| version string: CP2K version 2.3</div><div class=""> CP2K| source code revision number: 12343</div><div class=""> CP2K| is freely available from <a href="http://www.cp2k.org/" class="">http://www.cp2k.org/</a></div><div class=""> CP2K| Program compiled at Thu Feb 28 16:12:09 GMT 2013</div><div class=""> CP2K| Program compiled on popoca</div><div class=""> CP2K| Program compiled for Linux-x86-64-gfortran</div><div class=""> CP2K| Input file name mm.inp</div><div class=""><br class=""></div><div class=""> GLOBAL| Force Environment number 1</div><div class=""> GLOBAL| Basis set file name BASIS_SET</div><div class=""> GLOBAL| Geminal file name BASIS_GEMINAL</div><div class=""> GLOBAL| Potential file name POTENTIAL</div><div class=""> GLOBAL| MM Potential file name MM_POTENTIAL</div><div class=""> GLOBAL| Coordinate file name ionized.pdb</div><div class=""> GLOBAL| Method name CP2K</div><div class=""> GLOBAL| Project name phd2_md</div><div class=""> GLOBAL| Preferred FFT library FFTSG</div><div class=""> GLOBAL| Run type MD</div><div class=""> GLOBAL| All-to-all communication in single precision F</div><div class=""> GLOBAL| FFTs using library dependent lengths F</div><div class=""> GLOBAL| Global print level LOW</div><div class=""> GLOBAL| Total number of message passing processes 1</div><div class=""> GLOBAL| Number of threads for this process 1</div><div class=""> GLOBAL| This output is from process 0</div><div class=""><br class=""></div><div class=""> MEMORY| system memory details [Kb]</div><div class=""> MEMORY| rank 0 min max average</div><div class=""> MEMORY| MemTotal 132089732 132089732 132089732 132089732</div><div class=""> MEMORY| MemFree 2537384 2537384 2537384 2537384</div><div class=""> MEMORY| Buffers 407408 407408 407408 407408</div><div class=""> MEMORY| Cached 34948436 34948436 34948436 34948436</div><div class=""> MEMORY| Slab 732060 732060 732060 732060</div><div class=""> MEMORY| SReclaimable 581768 581768 581768 581768</div><div class=""> MEMORY| MemLikelyFree 38474996 38474996 38474996 38474996</div><div class=""><br class=""></div><div class=""> 49892 0</div><div class=""> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div class=""> 49893 0</div><div class=""> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div class=""> 49894 0</div><div class=""> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div class=""> 49895 0</div><div class=""> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div class=""> 49896 0</div><div class=""> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div class=""> 49897 0</div><div class=""> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div></div><div class="">"</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">I'm calling a PSF and PDF file that I know works. The error lies with the parsing of the </div><div class="">ion section (SOD and CLA).</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">My MM input is:</div><div class=""><br class=""></div><div class=""><div class="">&GLOBAL</div><div class=""> PRINT_LEVEL LOW</div><div class=""> PREFERRED_FFT_LIBRARY FFTSG</div><div class=""> PROJECT phd2_md</div><div class=""> RUN_TYPE MD</div><div class="">&END GLOBAL</div><div class=""><br class=""></div><div class="">&MOTION</div><div class=""> &MD</div><div class=""> ENSEMBLE NPT_I</div><div class=""> STEPS 6000</div><div class=""> TIMESTEP 0.48</div><div class=""> TEMPERATURE 298.0</div><div class=""> &THERMOSTAT</div><div class=""> TYPE NOSE</div><div class=""> REGION MASSIVE</div><div class=""> &NOSE</div><div class=""> TIMECON [wavenumber_t] 1000</div><div class=""> &END NOSE</div><div class=""> &END THERMOSTAT</div><div class=""> &PRINT</div><div class=""> &ENERGY</div><div class=""> FILENAME =phd2_md.ener</div><div class=""> &EACH</div><div class=""> MD 1</div><div class=""> &END EACH</div><div class=""> &END ENERGY</div><div class=""> &PROGRAM_RUN_INFO</div><div class=""> &EACH</div><div class=""> MD 1</div><div class=""> &END EACH</div><div class=""> &END PROGRAM_RUN_INFO</div><div class=""> &END PRINT</div><div class=""> &END MD</div><div class=""> &PRINT</div><div class=""> &TRAJECTORY</div><div class=""> FILENAME =phd2_md.xyz</div><div class=""> &EACH</div><div class=""> MD 1</div><div class=""> &END EACH</div><div class=""> &END TRAJECTORY</div><div class=""> &RESTART</div><div class=""> FILENAME =phd2_md.restart</div><div class=""> BACKUP_COPIES 1</div><div class=""> &EACH</div><div class=""> MD 10</div><div class=""> &END EACH</div><div class=""> &END RESTART</div><div class=""> &RESTART_HISTORY OFF</div><div class=""> &END RESTART_HISTORY</div><div class=""> &END PRINT</div><div class="">&END MOTION</div><div class=""><br class=""></div><div class="">&FORCE_EVAL</div><div class=""> METHOD FIST ! Using Molecular Mechanics</div><div class=""> &MM</div><div class=""> &FORCEFIELD</div><div class=""> parm_file_name par_all27_prot_lipid.inp</div><div class=""> parmtype CHM</div><div class=""> ei_scale14 1.0</div><div class=""> vdw_scale14 1.0</div><div class=""> &SPLINE</div><div class=""> emax_spline 1.0</div><div class=""> rcut_nb 12</div><div class=""> &END SPLINE</div><div class=""> &END FORCEFIELD</div><div class=""> &POISSON</div><div class=""> &EWALD</div><div class=""> ewald_type SPME</div><div class=""> alpha 0.44</div><div class=""> gmax 81</div><div class=""> &END EWALD</div><div class=""> &END POISSON</div><div class=""> &END MM</div><div class=""><br class=""></div><div class=""> &SUBSYS</div><div class=""> &CELL</div><div class=""> abc 80 80 80</div><div class=""> periodic xyz</div><div class=""> &END CELL</div><div class=""> &KIND H</div><div class=""> BASIS_SET DZVP-GTH-BLYP</div><div class=""> POTENTIAL GTH-BLYP-q1</div><div class=""> &END KIND</div><div class=""> &KIND O</div><div class=""> BASIS_SET DZVP-GTH-BLYP</div><div class=""> POTENTIAL GTH-BLYP-q6</div><div class=""> &END KIND</div><div class=""> &KIND N</div><div class=""> BASIS_SET DZVP-GTH-BLYP</div><div class=""> POTENTIAL GTH-BLYP-q5</div><div class=""> &END KIND</div><div class=""> &KIND C</div><div class=""> BASIS_SET DZVP-GTH-BLYP</div><div class=""> POTENTIAL GTH-BLYP-q4</div><div class=""> &END KIND</div><div class=""> &KIND Fe2</div><div class=""> BASIS_SET DZVP-MOLOPT-SR-GTH</div><div class=""> POTENTIAL DZVP-MOLOPT-SR-GTH</div><div class=""> &END KIND</div><div class=""><br class=""></div><div class=""> &TOPOLOGY</div><div class=""> CONNECTIVITY UPSF</div><div class=""> COORDINATE PDB</div><div class=""> COORD_FILE_NAME ionized.pdb</div><div class=""> CONN_FILE_NAME ionized.psf</div><div class=""> &END TOPOLOGY</div><div class=""> &END SUBSYS</div><div class="">&END FORCE_EVAL</div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div></div><div class=""><br class="webkit-block-placeholder"></div> -- <br class=""> You received this message because you are subscribed to the Google Groups "cp2k" group.<br class=""> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+uns...@googlegroups.com" class="">cp2k+uns...@googlegroups.com</a>.<br class=""> To post to this group, send email to <a href="mailto:cp...@googlegroups.com" class="">cp...@googlegroups.com</a>.<br class=""> Visit this group at <a href="http://groups.google.com/group/cp2k" class="">http://groups.google.com/group/cp2k</a>.<br class=""> For more options, visit <a href="https://groups.google.com/d/optout" class="">https://groups.google.com/d/optout</a>.<br class=""> </div></blockquote></div><br class=""></div></body></html>