<div dir="ltr"><div>After many more hours of searching for the cause of the problem I was able to identify it. </div><div><br></div><div>What made the search very difficult was also the misleading error message of CP2K (see previous mail), because it issued an error about missing angle terms where atom types where not fully expaned, but CP2K has truncated the atom types in the error message. This led me to believe that too long atom types or problems in the psf file are the cause of the problem. However, CP2K had correctly parsed the psf files and the full atom types (which had up to six characters).</div><div><br></div><div>From what I can tell the problem seems to be that the official CGenFF file contains comments which contain the "@" symbol, e.g. </div><div><div><br></div></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><div style="text-align: left;">CG2DC1 CG2DC1 CG2DC2 48.00 123.00 ! RETINOL 13DP, Pentadiene @@@@@ Kenno: 123.5-->123.0 @@@@@</div></div></blockquote><div><br></div><div>Which seems to cause CP2K to ignore the entire parameter section. After delete the @-symbols CP2K is running as it should.</div><div><br></div><div>Best wishes,</div><div>Jadzia</div><div><br></div><br><br>On Monday, January 1, 2018 at 3:18:10 PM UTC+1, Jadzia wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Happy new year to everyone,<div><br></div><div>I have a closely related problem to the one above. I get the error message:</div><div><br></div><div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><br> FORCEFIELD| Missing Angle (NG2R,CG2R,OG2R)<br> FORCEFIELD| Missing Angle (CG2R,CG2R,OG2R)<br> FORCEFIELD| Missing Angle (OG2R,CG2R,HGR5)<br> *****************************<wbr>******************************<wbr>********************<br> * ___ *<br> * / \ *<br> * [ABORT] *<br> * \___/ Missing critical ForceField parameters! *<br> * | *<br> * O/| *<br> * /| | *<br> * / \ force_fields_util.F:387 *<br> *****************************<wbr>******************************<wbr>********************</blockquote></div><div><br></div><div><br></div><div>But in my PSF file I do not have any atoms of the type these types (e.g. NG2R), only longer types (e.g. NG2R50). These are the default CGenFF atom types. </div><div style="text-align:left"><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div style="text-align:left"><br></div><div><div style="text-align:left"><font face="courier new, monospace" size="1">PSF</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 1 !NTITLE</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> REMARKS VMD-generated NAMD/X-Plor PSF structure file</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"><br></font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 1821 !NATOM</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 1 LIG 1 LIG N1Q NG2S1 -0.495000 14.0067 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 2 LIG 1 LIG C1Q CG2O1 0.464000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 3 LIG 1 LIG O1Q OG2D1 -0.509000 15.9994 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 4 LIG 1 LIG C2Q CG331 -0.269000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 5 LIG 1 LIG C3Q CG311 0.150000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 6 LIG 1 LIG C4Q CG2R61 0.005000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 7 LIG 1 LIG C5Q CG2R61 -0.111000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 8 LIG 1 LIG C6Q CG2R61 -0.114000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 9 LIG 1 LIG C7Q CG2R67 -0.004000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 10 LIG 1 LIG C8Q CG2R61 -0.114000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 11 LIG 1 LIG C9Q CG2R61 -0.111000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 12 LIG 1 LIG C10Q CG2R67 -0.004000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 13 LIG 1 LIG C11Q CG2R61 -0.114000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 14 LIG 1 LIG C12Q CG2R61 -0.114000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 15 LIG 1 LIG C13Q CG2R61 -0.115000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 16 LIG 1 LIG C14Q CG2R61 -0.114000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 17 LIG 1 LIG C15Q CG2R61 -0.114000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 18 LIG 1 LIG C16Q CG321 -0.136000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 19 LIG 1 LIG S1Q SG311 -0.076000 32.0650 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 20 LIG 1 LIG C17Q CG2R53 0.562000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 21 LIG 1 LIG N2Q NG2R50 -0.355000 14.0067 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 22 LIG 1 LIG N3Q NG2R50 -0.249000 14.0067 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 23 LIG 1 LIG C18Q CG2R57 0.545000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 24 LIG 1 LIG O2Q OG2R50 -0.465000 15.9994 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 25 LIG 1 LIG C19Q CG2R57 0.247000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 26 LIG 1 LIG C20Q CG2R51 -0.179000 12.0107 0</font></div></div><div><div style="text-align:left"><font face="courier new, monospace" size="1"> 27 LIG 1 LIG C21Q CG2R51 -0.276000 12.0107 0</font></div></div></blockquote></div><div style="text-align:left"><br></div><div>And for all atom types I do have parameters in the prm file. </div><div><br></div><div>I have already tried to shift the position of the columns, in vain. In the cp2k input file I have specified: CONN_FILE_FORMAT upsf</div><div><br></div><div>Any help is highly appreciated. I use cp2k version 5.1. </div><div><br></div><div>Thank you very much,</div><div>Jadzia</div><div><br></div><div><br><br>On Friday, June 1, 2007 at 4:59:26 PM UTC+2, Teo wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex">Thanks for the files Toon,<p>it needs a COORD section mostly because the conversion to the new <br>input was not fully<br>completed for the MC module.</p><p>Teo<br>On 1 Jun 2007, at 15:18, Toon wrote:</p><p>><br>> My apologies for the inconveinience. This is a more complete<br>> description of the problem: I'm now running a cp2k compilation checked<br>> out this morning. I have a problem that seems to be related to these<br>> two input lines:<br>><br>> COORDINATE XYZ<br>> COORD_FILE_NAME <a href="http://geometry.xyz" rel="nofollow" target="_blank" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fgeometry.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNE5Pxh0mbyDajJ_J9X7wxdo55_fRA';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fgeometry.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNE5Pxh0mbyDajJ_J9X7wxdo55_fRA';return true;">geometry.xyz</a><br>><br>> The error given by cp2k looks like this:<br>><br>> ...<br>> MC| The moves will not be biased,<br>> MC| A full energy calculation will be done at every step.<br>> MC| 4 swap insertions will be attempted per molecular swap move<br>><br>> File name mc.inp<br>><br>><br>> *****************************<wbr>*******************<br>> *** ERROR in mc_types.F/mc_input_file_<wbr>create ***<br>> *****************************<wbr>*******************<br>><br>> *** Could not find &END after &COORD (make sure & is the first in the<br>> ***<br>> *** same column after &COORD)<br>> ***<br>><br>><br>> ===== Routine Calling Stack =====<br>><br>> 1 CP2K<br>><br>> CP2K| Stopped by process<br>> number 0<br>> CP2K| Abnormal program termination<br>><br>> Aborted<br>><br>><br>> It appears that the MC code requires the COORD section to be used<br>> instead of other means of defining the molecular geometry. These are<br>> all the input files:<br>><br>> mc.inp:<br>><br>> &FORCE_EVAL<br>><br>> METHOD Quickstep<br>> &DFT<br>> &QS<br>> METHOD PM3<br>> EPS_DEFAULT 1.0E-12<br>> EPS_GVG 1.0E-6<br>> EPS_PGF_ORB 1.0E-6<br>> &END QS<br>> &SCF<br>> EPS_SCF 1.0E-6<br>> MAX_SCF 150<br>> SCF_GUESS atomic<br>> &END SCF<br>> &END DFT<br>><br>> &SUBSYS<br>> &CELL<br>> ABC 7.800000 7.800000 7.800000<br>> UNIT ANGSTROM<br>> &END CELL<br>> &TOPOLOGY<br>> COORDINATE XYZ<br>> COORD_FILE_NAME <a href="http://init.xyz" rel="nofollow" target="_blank" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Finit.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHQ201bTM4N_9-AhMJCfzR_6uT6MA';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Finit.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHQ201bTM4N_9-AhMJCfzR_6uT6MA';return true;">init.xyz</a><br>> CONNECTIVITY MOL_SET<br>> &MOL_SET<br>> &MOLECULE<br>> NMOL 8<br>> CONN_FILE_NAME single.psf<br>> CONNECTIVITY UPSF<br>> &END<br>> &END<br>> &END TOPOLOGY<br>> &PRINT<br>> &TOPOLOGY_INFO<br>> EACH 1<br>> PSF_INFO T<br>> &END TOPOLOGY_INFO<br>> &END PRINT<br>> &END SUBSYS<br>> &END FORCE_EVAL<br>><br>> &GLOBAL<br>> FFT_LIB FFTSG<br>> PROJECT mc<br>> RUN_TYPE MC<br>> &END GLOBAL<br>><br>> &MOTION<br>> &MC<br>> IUPTRANS 100<br>> IUPVOLUME 100<br>> LBIAS no<br>> LSTOP no<br>> NMOVES 1<br>> NSTEP 10<br>> PMSWAP 0.0<br>> PMSWAP_MOL 1.0<br>> PMTRAION 0.00<br>> PMTRAION_MOL 1.0<br>> PMTRANS 0.5<br>> PMTRANS_MOL 1.0<br>> PMROT_MOL 1.0<br>> PMVOLUME 0.2<br>> PMVOL_BOX 1.0<br>> PRESSURE 1.013<br>> ENSEMBLE traditional<br>> RESTART no<br>> RESTART_FILE_NAME mc_restart_1<br>> RMDIHEDRAL 1.0<br>> RMANGLE 3.0<br>> RMBOND 0.074<br>> RMROT 26.0<br>> RMTRANS 0.38<br>> RMVOLUME 1.0<br>> TEMPERATURE 298.0<br>> IPRINT 1<br>> AVBMC_ATOM 1<br>> NSWAPMOVES 4<br>> PMAVBMC 0.5<br>> PMAVBMC_MOL 1.0<br>> AVBMC_RMIN 2.0<br>> AVBMC_RMAX 4.0<br>> PBIAS 0.5<br>> VIRIAL_TEMPS 300.0<br>> &END MC<br>> &PRINT<br>> &TRAJECTORY<br>> EACH 5<br>> &END TRAJECTORY<br>> &END PRINT<br>> &END MOTION<br>><br>> This is single.psf<br>><br>> PSF<br>><br>> 1 !NTITLE<br>> None<br>><br>> 5 !NATOM<br>> 1 NAME 1 NAME C C 0.0 12.010700 0<br>> 2 NAME 1 NAME H H 0.0 1.007940 0<br>> 3 NAME 1 NAME H H 0.0 1.007940 0<br>> 4 NAME 1 NAME H H 0.0 1.007940 0<br>> 5 NAME 1 NAME H H 0.0 1.007940 0<br>><br>> 4 !NBOND<br>> 2 1 3 1 4 1 5 1<br>><br>> 6 !NTHETA<br>> 4 1 2 5 1 2 3 1 2<br>> 5 1 4 4 1 3 5 1 3<br>><br>> 0 !NPHI<br>><br>> 0 !NIMPHI<br>><br>> 0 !NDON<br>><br>> 0 !NACC<br>><br>> 0 !NNB<br>><br>><br>> This is <a href="http://init.xyz" rel="nofollow" target="_blank" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Finit.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHQ201bTM4N_9-AhMJCfzR_6uT6MA';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Finit.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHQ201bTM4N_9-AhMJCfzR_6uT6MA';return true;">init.xyz</a><br>><br>> 40<br>> i = 200, E = 22.6433415965<br>> C 6.9039075582 2.2556748672 0.6684090906<br>> H 7.5807042939 2.9514646584 0.1778234170<br>> H 6.4359114825 1.6148018511 -0.0751255788<br>> H 6.1411834553 2.8077213762 1.2123856443<br>> H 7.4649087760 1.6437421117 1.3661103663<br>> C 6.9115470203 6.1425921064 2.1589360246<br>> H 7.6276416557 6.8618026951 2.5486690023<br>> H 7.4061522809 5.4950308617 1.4429986121<br>> H 6.1001618632 6.6677780946 1.6615302422<br>> H 6.5170086641 5.5418353691 2.9752995498<br>> C 0.8124559617 6.2174060423 6.1085385115<br>> H 0.9682759157 6.3527520522 5.0415332216<br>> H -0.0050460555 6.8521178205 6.4438165561<br>> H 1.7204472263 6.4844467269 6.6359163451<br>> H 0.5776741793 5.1779744893 6.3188571695<br>> C 4.6568183079 8.5306984679 4.5589000442<br>> H 5.4014171220 8.0383130247 5.1798098710<br>> H 4.0720357993 7.7856805661 4.0247749152<br>> H 5.1510519252 9.1888538100 3.8480745892<br>> H 3.9962925018 9.1156867542 5.1893066759<br>> C 3.0026367985 4.6804958145 2.1341762406<br>> H 2.5872117262 5.3961909512 2.8398055744<br>> H 3.5973758287 3.9441956718 2.6702281645<br>> H 3.6343783322 5.2012588593 1.4230404511<br>> H 2.1983186479 4.1851221980 1.5958594440<br>> C 3.0357598254 8.6354879819 8.5015934277<br>> H 2.2355644284 8.1192114793 9.0268620523<br>> H 3.7132001125 7.9084963590 8.0584302518<br>> H 3.5842911872 9.2497091821 9.2067104274<br>> H 2.6159490587 9.2689729491 7.7228475826<br>> C 8.5668539873 2.2952643674 4.5588139458<br>> H 9.3584593729 2.7884860822 5.1172331341<br>> H 9.0003049169 1.6000473260 3.8438410104<br>> H 7.9715191708 3.0389332591 4.0342037810<br>> H 7.9309384985 1.7492402764 5.2468924719<br>> C 4.7102978422 4.6594015643 6.0167776096<br>> H 5.5013143603 4.2000713116 5.4279574197<br>> H 5.1427927774 5.3339687406 6.7519655838<br>> H 4.1333208145 3.8893804981 6.5228756168<br>> H 4.0540983796 5.2195783822 5.3595115407<br>><br>><br>><br>><br>> ></p><p></p><p></p><p></p><p></p></blockquote></div></div></blockquote></div>