<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> *******************************************************************************<br> * ___ *<br> * / \ *<br> * [ABORT] *<br> * \___/ Missing critical ForceField parameters! *<br> * | *<br> * O/| *<br> * /| | *<br> * / \ force_fields_util.F:387 *<br> *******************************************************************************</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" target="_blank" rel="nofollow" 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" target="_blank" rel="nofollow" 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" target="_blank" rel="nofollow" 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>