<div dir="ltr"><div><div><div><div><div><div>OK, update: from what I understand, CP2K parses PSF<br></div>atom types up to 4 characters. <br>The CHARMM general force field uses a CGenFF naming<br>scheme with 5 character strings, which has been known <br>to cause problems in NAMD (and is solved by adding the<br>command <br></div>PSF NAMD) <br><br><br></div>I edited the 5-character strings to 4-characters (parsed by <br>CP2K) and changed all names in the parameter file.<br><br></div>Now I get another error<br><br><br><br> ****************************************************************************<br> *** 20:02:00 ERRORL2 in cp_parser_methods:parser_get_string processor 0 ***<br> *** err=-300 A string type object was expected, found end of line ***<br> *** file:'par_all27_prot_lipid.inp' line: 680 col: 30 ***<br> ****************************************************************************<br><br><br> ===== Routine Calling Stack =====<br><br> 5 read_force_field_charmm<br> 4 force_field_control<br> 3 fist_init<br> 2 fist_create_force_env<br> 1 CP2K<br> CP2K| A string type object was expected, found end of line file:'par_all27_prot_lipid.inp' line: 680 col: 30<br> CP2K| Abnormal program termination, stopped by process number 0<br><br><br><br></div>I attach the parameter file for reference. <br><br></div>I have checked line 680 and see nothing anomalous. <br><br><br><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Feb 12, 2015 at 2:07 PM, Christian Jorgensen <span dir="ltr"><<a href="mailto:chri...@gmail.com" target="_blank">chri...@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Sorry I do not understand why the tone on<div>this board is like this. I'm simply asking for help.</div><div><br></div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><div><div class="h5"><br><div class="gmail_quote">On Thu, Feb 12, 2015 at 7:16 AM, Teodoro Laino <span dir="ltr"><<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">report this to the proper mailing list.<div><div><div><br><div><blockquote type="cite"><div>On 11 Feb 2015, at 23:04, Christian Jorgensen <<a href="mailto:chri...@gmail.com" target="_blank">chri...@gmail.com</a>> wrote:</div><br><div><div dir="ltr" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div>ATOM 49880 SOD SOD I 37 21.151 0.526 -30.628 1.00 0.00 ION NA</div><div>ATOM 49881 SOD SOD I 38 24.667 -35.051 19.114 1.00 0.00 ION NA</div><div>ATOM 49882 SOD SOD I 39 -12.620 2.426 26.969 1.00 0.00 ION NA</div><div>ATOM 49883 SOD SOD I 40 -10.705 -33.380 -11.158 1.00 0.00 ION NA</div><div>ATOM 49884 SOD SOD I 41 -19.491 29.350 -34.679 1.00 0.00 ION NA</div><div>ATOM 49885 SOD SOD I 42 40.802 -30.866 10.911 1.00 0.00 ION NA</div><div>ATOM 49886 SOD SOD I 43 -21.411 -20.389 17.270 1.00 0.00 ION NA</div><div>ATOM 49887 SOD SOD I 44 13.100 24.287 18.857 1.00 0.00 ION NA</div><div>ATOM 49888 SOD SOD I 45 33.628 30.716 18.333 1.00 0.00 ION NA</div><div>ATOM 49889 SOD SOD I 46 14.256 -31.556 -9.097 1.00 0.00 ION NA</div><div>ATOM 49890 SOD SOD I 47 -1.600 38.825 28.079 1.00 0.00 ION NA</div><div>ATOM 49891 SOD SOD I 48 26.911 -9.319 19.217 1.00 0.00 ION NA</div><div>ATOM 49892 CLA CLA I 49 -21.849 -29.233 -4.389 1.00 0.00 ION CL</div><div>ATOM 49893 CLA CLA I 50 -27.778 19.207 -8.907 1.00 0.00 ION CL</div><div>ATOM 49894 CLA CLA I 51 -1.036 -18.525 -33.557 1.00 0.00 ION CL</div><div>ATOM 49895 CLA CLA I 52 -37.955 23.751 -9.529 1.00 0.00 ION CL</div><div>ATOM 49896 CLA CLA I 53 -15.636 -34.005 12.873 1.00 0.00 ION CL</div><div>ATOM 49897 CLA CLA I 54 40.122 21.296 -26.349 1.00 0.00 ION CL</div><div>ATOM 49898 CLA CLA I 55 32.593 -9.101 17.836 1.00 0.00 ION CL</div><div>ATOM 49899 CLA CLA I 56 8.168 -24.215 8.246 1.00 0.00 ION CL</div><div>ATOM 49900 CLA CLA I 57 -4.530 -32.691 -6.031 1.00 0.00 ION CL</div><div>ATOM 49901 CLA CLA I 58 -14.998 37.422 2.603 1.00 0.00 ION CL</div><div>ATOM 49902 CLA CLA I 59 -22.559 -24.866 -37.160 1.00 0.00 ION CL</div><div>ATOM 49903 CLA CLA I 60 22.442 -17.653 -37.184 1.00 0.00 ION CL</div><div>ATOM 49904 CLA CLA I 61 -31.657 0.756 -22.411 1.00 0.00 ION CL</div><div>ATOM 49905 CLA CLA I 62 -25.707 4.569 26.200 1.00 0.00 ION CL</div><div>ATOM 49906 CLA CLA I 63 9.816 21.844 -29.523 1.00 0.00 ION CL</div><div>ATOM 49907 CLA CLA I 64 20.348 15.655 31.373 1.00 0.00 ION CL</div><div>ATOM 49908 CLA CLA I 65 -33.471 28.927 25.816 1.00 0.00 ION CL</div><div>ATOM 49909 CLA CLA I 66 -23.076 -36.320 -14.581 1.00 0.00 ION CL</div><div>ATOM 49910 CLA CLA I 67 11.228 23.055 26.442 1.00 0.00 ION CL</div><div>ATOM 49911 CLA CLA I 68 -31.967 -25.220 12.122 1.00 0.00 ION CL</div><div>ATOM 49912 CLA CLA I 69 7.122 -32.163 -23.902 1.00 0.00 ION CL</div><div>ATOM 49913 CLA CLA I 70 -30.542 -17.921 15.502 1.00 0.00 ION CL</div><div>ATOM 49914 CLA CLA I 71 -35.163 -32.044 11.857 1.00 0.00 ION CL</div><div>ATOM 49915 CLA CLA I 72 -1.340 -18.251 -21.790 1.00 0.00 ION CL</div><div><br></div><div><br></div><div>In relation to the error</div><div><br></div><div><br></div><div><div style="font-size:13px"><div> 49892 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div> 49893 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div> 49894 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div> 49895 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div> 49896 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div> 49897 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div></div><div style="font-size:13px">"</div></div><div><br></div><div><br></div><div>How can this be? I've generated this with the standard PSFGEN / Ionize plugin written</div><div>for VMD. </div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><br><div class="gmail_quote">On Wed, Feb 11, 2015 at 9:14 PM, Christian Jorgensen<span> </span><span dir="ltr"><<a href="mailto:chri...@gmail.com" target="_blank">chri...@gmail.com</a>></span><span> </span>wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><p dir="ltr">Hello Dr Laino</p><p dir="ltr">This is a problem with the ions. The atom indices it is warning about are all chlorine added to achieve electrical neutrality ( in VMD with Psfgen for NAMD)</p><p dir="ltr">I do not understand because I've used the standard procedure from Psfgen</p><div><div><div class="gmail_quote">On 11 Feb 2015 20:57, "Teodoro Laino" <<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word">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><br></div><div>the fact your PSF or PDB may work with other codes means only that such codes are not performing tight checks.</div><div><br></div><div>Teo</div><div><br><div><blockquote type="cite"><div>On 11 Feb 2015, at 18:51, cjor <<a href="mailto:chri...@gmail.com" target="_blank">chri...@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Hello, <div>I'm trying to run a QMMM simulation with CP2K based on a CHARMM FF MD simulation.</div><div><br></div><div>I first tried to run MM to see it works, but I get the following error:</div><div><br></div><div><br></div><div>"</div><div><div> CP2K| version string: CP2K version 2.3</div><div> CP2K| source code revision number: 12343</div><div> CP2K| is freely available from <span> </span><a href="http://www.cp2k.org/" target="_blank">http://www.cp2k.org/</a></div><div> CP2K| Program compiled at Thu Feb 28 16:12:09 GMT 2013</div><div> CP2K| Program compiled on popoca</div><div> CP2K| Program compiled for Linux-x86-64-gfortran</div><div> CP2K| Input file name mm.inp</div><div><br></div><div> GLOBAL| Force Environment number 1</div><div> GLOBAL| Basis set file name BASIS_SET</div><div> GLOBAL| Geminal file name BASIS_GEMINAL</div><div> GLOBAL| Potential file name POTENTIAL</div><div> GLOBAL| MM Potential file name MM_POTENTIAL</div><div> GLOBAL| Coordinate file name ionized.pdb</div><div> GLOBAL| Method name CP2K</div><div> GLOBAL| Project name phd2_md</div><div> GLOBAL| Preferred FFT library FFTSG</div><div> GLOBAL| Run type MD</div><div> GLOBAL| All-to-all communication in single precision F</div><div> GLOBAL| FFTs using library dependent lengths F</div><div> GLOBAL| Global print level LOW</div><div> GLOBAL| Total number of message passing processes 1</div><div> GLOBAL| Number of threads for this process 1</div><div> GLOBAL| This output is from process 0</div><div><br></div><div> MEMORY| system memory details [Kb]</div><div> MEMORY| rank 0 min max average</div><div> MEMORY| MemTotal 132089732 132089732 132089732 132089732</div><div> MEMORY| MemFree 2537384 2537384 2537384 2537384</div><div> MEMORY| Buffers 407408 407408 407408 407408</div><div> MEMORY| Cached 34948436 34948436 34948436 34948436</div><div> MEMORY| Slab 732060 732060 732060 732060</div><div> MEMORY| SReclaimable 581768 581768 581768 581768</div><div> MEMORY| MemLikelyFree 38474996 38474996 38474996 38474996</div><div><br></div><div> 49892 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div> 49893 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div> 49894 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div> 49895 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div> 49896 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div><div> 49897 0</div><div> Two molecules have been defined as identical molecules but atoms mismatch charges!!</div></div><div>"</div><div><br></div><div><br></div><div><br></div><div><br></div><div>I'm calling a PSF and PDF file that I know works. The error lies with the parsing of the </div><div>ion section (SOD and CLA).</div><div><br></div><div><br></div><div><br></div><div><br></div><div>My MM input is:</div><div><br></div><div><div>&GLOBAL</div><div> <span> </span>PRINT_LEVEL LOW</div><div> <span> </span>PREFERRED_FFT_LIBRARY FFTSG</div><div> <span> </span>PROJECT phd2_md</div><div> <span> </span>RUN_TYPE MD</div><div>&END GLOBAL</div><div><br></div><div>&MOTION</div><div> <span> </span>&MD</div><div> <span> </span>ENSEMBLE NPT_I</div><div> <span> </span>STEPS 6000</div><div> <span> </span>TIMESTEP 0.48</div><div> <span> </span>TEMPERATURE 298.0</div><div> <span> </span>&THERMOSTAT</div><div> <span> </span>TYPE NOSE</div><div> <span> </span>REGION MASSIVE</div><div> <span> </span>&NOSE</div><div> <span> </span>TIMECON [wavenumber_t] 1000</div><div> <span> </span>&END NOSE</div><div> <span> </span>&END THERMOSTAT</div><div> <span> </span>&PRINT</div><div> <span> </span>&ENERGY</div><div> <span> </span>FILENAME =phd2_md.ener</div><div> <span> </span>&EACH</div><div> <span> </span>MD 1</div><div> <span> </span>&END EACH</div><div> <span> </span>&END ENERGY</div><div> <span> </span>&PROGRAM_RUN_INFO</div><div> <span> </span>&EACH</div><div> <span> </span>MD 1</div><div> <span> </span>&END EACH</div><div> <span> </span>&END PROGRAM_RUN_INFO</div><div> <span> </span>&END PRINT</div><div> <span> </span>&END MD</div><div> <span> </span>&PRINT</div><div> <span> </span>&TRAJECTORY</div><div> <span> </span>FILENAME =phd2_md.xyz</div><div> <span> </span>&EACH</div><div> <span> </span>MD 1</div><div> <span> </span>&END EACH</div><div> <span> </span>&END TRAJECTORY</div><div> <span> </span>&RESTART</div><div> <span> </span>FILENAME =phd2_md.restart</div><div> <span> </span>BACKUP_COPIES 1</div><div> <span> </span>&EACH</div><div> <span> </span>MD 10</div><div> <span> </span>&END EACH</div><div> <span> </span>&END RESTART</div><div> <span> </span>&RESTART_HISTORY OFF</div><div> <span> </span>&END RESTART_HISTORY</div><div> <span> </span>&END PRINT</div><div>&END MOTION</div><div><br></div><div>&FORCE_EVAL</div><div> <span> </span>METHOD FIST ! Using Molecular Mechanics</div><div> <span> </span>&MM</div><div> <span> </span>&FORCEFIELD</div><div> <span> </span>parm_file_name par_all27_prot_lipid.inp</div><div> <span> </span>parmtype CHM</div><div> <span> </span>ei_scale14 1.0</div><div> <span> </span>vdw_scale14 1.0</div><div> <span> </span>&SPLINE</div><div> <span> </span>emax_spline 1.0</div><div> <span> </span>rcut_nb 12</div><div> <span> </span>&END SPLINE</div><div> <span> </span>&END FORCEFIELD</div><div> <span> </span>&POISSON</div><div> <span> </span>&EWALD</div><div> <span> </span>ewald_type SPME</div><div> <span> </span>alpha 0.44</div><div> <span> </span>gmax 81</div><div> <span> </span>&END EWALD</div><div> <span> </span>&END POISSON</div><div> <span> </span>&END MM</div><div><br></div><div> <span> </span>&SUBSYS</div><div> <span> </span>&CELL</div><div> <span> </span>abc 80 80 80</div><div> <span> </span>periodic xyz</div><div> <span> </span>&END CELL</div><div> <span> </span>&KIND H</div><div> <span> </span>BASIS_SET DZVP-GTH-BLYP</div><div> <span> </span>POTENTIAL GTH-BLYP-q1</div><div> <span> </span>&END KIND</div><div> <span> </span>&KIND O</div><div> <span> </span>BASIS_SET DZVP-GTH-BLYP</div><div> <span> </span>POTENTIAL GTH-BLYP-q6</div><div> <span> </span>&END KIND</div><div> <span> </span>&KIND N</div><div> <span> </span>BASIS_SET DZVP-GTH-BLYP</div><div> <span> </span>POTENTIAL GTH-BLYP-q5</div><div> <span> </span>&END KIND</div><div> <span> </span>&KIND C</div><div> <span> </span>BASIS_SET DZVP-GTH-BLYP</div><div> <span> </span>POTENTIAL GTH-BLYP-q4</div><div> <span> </span>&END KIND</div><div> <span> </span>&KIND Fe2</div><div> <span> </span>BASIS_SET DZVP-MOLOPT-SR-GTH</div><div> <span> </span>POTENTIAL DZVP-MOLOPT-SR-GTH</div><div> <span> </span>&END KIND</div><div><br></div><div> <span> </span>&TOPOLOGY</div><div> <span> </span>CONNECTIVITY UPSF</div><div> <span> </span>COORDINATE PDB</div><div> <span> </span>COORD_FILE_NAME ionized.pdb</div><div> <span> </span>CONN_FILE_NAME ionized.psf</div><div> <span> </span>&END TOPOLOGY</div><div> <span> </span>&END SUBSYS</div><div>&END FORCE_EVAL</div></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div><div><br></div>--<span> </span><br>You received this message because you are subscribed to the Google Groups "cp2k" group.<br>To unsubscribe from this group and stop receiving emails from it, send an email to<span> </span><a href="mailto:cp2k+uns...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a>.<br>To post to this group, send email to<span> </span><a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br>Visit this group at<span> </span><a href="http://groups.google.com/group/cp2k" target="_blank">http://groups.google.com/group/cp2k</a>.<br>For more options, visit<span> </span><a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/optout</a>.<br></div></blockquote></div><br></div></div><div><br></div>--<span> </span><br>You received this message because you are subscribed to a topic in the Google Groups "cp2k" group.<br>To unsubscribe from this topic, visit<span> </span><a href="https://groups.google.com/d/topic/cp2k/kkfMLpVx2Xo/unsubscribe" target="_blank">https://groups.google.com/d/topic/cp2k/kkfMLpVx2Xo/unsubscribe</a>.<br>To unsubscribe from this group and all its topics, send an email to<span> </span><a href="mailto:cp2k+uns...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a>.<br>To post to this group, send email to<span> </span><a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br>Visit this group at<span> </span><a href="http://groups.google.com/group/cp2k" target="_blank">http://groups.google.com/group/cp2k</a>.<br>For more options, visit<span> </span><a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/optout</a>.<br></blockquote></div></div></div></blockquote></div><br><br clear="all"><div><br></div>--<span> </span><br><div><div dir="ltr"><div>_______</div><div><br></div>Christian Jørgensen</div></div></div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><br></div><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">--<span> </span></span><br 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style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">For more options, visit<span> </span></span><a href="https://groups.google.com/d/optout" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">https://groups.google.com/d/optout</a><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">.</span></div></blockquote></div><br></div></div></div></div><div><div>
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</div></div></blockquote></div><br><br clear="all"><div><br></div></div></div><span class="HOEnZb"><font color="#888888">-- <br><div><div dir="ltr"><div>_______</div><div><br></div>Christian Jørgensen</div></div>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature"><div dir="ltr"><div>_______</div><div><br></div>Christian Jørgensen</div></div>
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