[CP2K:6095] Topology error QMMM or MM
hut... at chem.uzh.ch
hut... at chem.uzh.ch
Fri Feb 13 09:57:18 UTC 2015
Hi
thank you for sharing the insight and context for this problem.
The contribution is appreciated.
best regards
Juerg
PS: Unfortunately, I cannot help with the follow up problem.
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Juerg Hutter Phone : ++41 44 635 4491
Institut für Chemie C FAX : ++41 44 635 6838
Universität Zürich E-mail: hut... at chem.uzh.ch
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
---------------------------------------------------------------
-----cp... at googlegroups.com wrote: -----To: cp... at googlegroups.com
From: Christian Jorgensen
Sent by: cp... at googlegroups.com
Date: 02/12/2015 09:16PM
Subject: Re: [CP2K:6095] Topology error QMMM or MM
OK, update: from what I understand, CP2K parses PSF
atom types up to 4 characters.
The CHARMM general force field uses a CGenFF naming
scheme with 5 character strings, which has been known
to cause problems in NAMD (and is solved by adding the
command
PSF NAMD)
I edited the 5-character strings to 4-characters (parsed by
CP2K) and changed all names in the parameter file.
Now I get another error
****************************************************************************
*** 20:02:00 ERRORL2 in cp_parser_methods:parser_get_string processor 0 ***
*** err=-300 A string type object was expected, found end of line ***
*** file:'par_all27_prot_lipid.inp' line: 680 col: 30 ***
****************************************************************************
===== Routine Calling Stack =====
5 read_force_field_charmm
4 force_field_control
3 fist_init
2 fist_create_force_env
1 CP2K
CP2K| A string type object was expected, found end of line file:'par_all27_prot_lipid.inp' line: 680 col: 30
CP2K| Abnormal program termination, stopped by process number 0
I attach the parameter file for reference.
I have checked line 680 and see nothing anomalous.
On Thu, Feb 12, 2015 at 2:07 PM, Christian Jorgensen <chri... at gmail.com> wrote:
Sorry I do not understand why the tone onthis board is like this. I'm simply asking for help.
On Thu, Feb 12, 2015 at 7:16 AM, Teodoro Laino <teodor... at gmail.com> wrote:
report this to the proper mailing list.
On 11 Feb 2015, at 23:04, Christian Jorgensen <chri... at gmail.com> wrote:
ATOM 49880 SOD SOD I 37 21.151 0.526 -30.628 1.00 0.00 ION NAATOM 49881 SOD SOD I 38 24.667 -35.051 19.114 1.00 0.00 ION NAATOM 49882 SOD SOD I 39 -12.620 2.426 26.969 1.00 0.00 ION NAATOM 49883 SOD SOD I 40 -10.705 -33.380 -11.158 1.00 0.00 ION NAATOM 49884 SOD SOD I 41 -19.491 29.350 -34.679 1.00 0.00 ION NAATOM 49885 SOD SOD I 42 40.802 -30.866 10.911 1.00 0.00 ION NAATOM 49886 SOD SOD I 43 -21.411 -20.389 17.270 1.00 0.00 ION NAATOM 49887 SOD SOD I 44 13.100 24.287 18.857 1.00 0.00 ION NAATOM 49888 SOD SOD I 45 33.628 30.716 18.333 1.00 0.00 ION NAATOM 49889 SOD SOD I 46 14.256 -31.556 -9.097 1.00 0.00 ION NAATOM 49890 SOD SOD I 47 -1.600 38.825 28.079 1.00 0.00 ION NAATOM 49891 SOD SOD I 48 26.911 -9.319 19.217 1.00 0.00 ION NAATOM 49892 CLA CLA I 49 -21.849 -29.233 -4.389 1.00 0.00 ION CLATOM 49893 CLA CLA I 50 -27.778 19.207 -8.907 1.00 0.00 ION CLATOM 49894 CLA CLA I 51 -1.036 -18.525 -33.557 1.00 0.00 ION CLATOM 49895 CLA CLA I 52 -37.955 23.751 -9.529 1.00 0.00 ION CLATOM 49896 CLA CLA I 53 -15.636 -34.005 12.873 1.00 0.00 ION CLATOM 49897 CLA CLA I 54 40.122 21.296 -26.349 1.00 0.00 ION CLATOM 49898 CLA CLA I 55 32.593 -9.101 17.836 1.00 0.00 ION CLATOM 49899 CLA CLA I 56 8.168 -24.215 8.246 1.00 0.00 ION CLATOM 49900 CLA CLA I 57 -4.530 -32.691 -6.031 1.00 0.00 ION CLATOM 49901 CLA CLA I 58 -14.998 37.422 2.603 1.00 0.00 ION CLATOM 49902 CLA CLA I 59 -22.559 -24.866 -37.160 1.00 0.00 ION CLATOM 49903 CLA CLA I 60 22.442 -17.653 -37.184 1.00 0.00 ION CLATOM 49904 CLA CLA I 61 -31.657 0.756 -22.411 1.00 0.00 ION CLATOM 49905 CLA CLA I 62 -25.707 4.569 26.200 1.00 0.00 ION CLATOM 49906 CLA CLA I 63 9.816 21.844 -29.523 1.00 0.00 ION CLATOM 49907 CLA CLA I 64 20.348 15.655 31.373 1.00 0.00 ION CLATOM 49908 CLA CLA I 65 -33.471 28.927 25.816 1.00 0.00 ION CLATOM 49909 CLA CLA I 66 -23.076 -36.320 -14.581 1.00 0.00 ION CLATOM 49910 CLA CLA I 67 11.228 23.055 26.442 1.00 0.00 ION CLATOM 49911 CLA CLA I 68 -31.967 -25.220 12.122 1.00 0.00 ION CLATOM 49912 CLA CLA I 69 7.122 -32.163 -23.902 1.00 0.00 ION CLATOM 49913 CLA CLA I 70 -30.542 -17.921 15.502 1.00 0.00 ION CLATOM 49914 CLA CLA I 71 -35.163 -32.044 11.857 1.00 0.00 ION CLATOM 49915 CLA CLA I 72 -1.340 -18.251 -21.790 1.00 0.00 ION CL
In relation to the error
49892 0 Two molecules have been defined as identical molecules but atoms mismatch charges!! 49893 0 Two molecules have been defined as identical molecules but atoms mismatch charges!! 49894 0 Two molecules have been defined as identical molecules but atoms mismatch charges!! 49895 0 Two molecules have been defined as identical molecules but atoms mismatch charges!! 49896 0 Two molecules have been defined as identical molecules but atoms mismatch charges!! 49897 0 Two molecules have been defined as identical molecules but atoms mismatch charges!!"
How can this be? I've generated this with the standard PSFGEN / Ionize plugin writtenfor VMD.
On Wed, Feb 11, 2015 at 9:14 PM, Christian Jorgensen <chri... at gmail.com> wrote:
Hello Dr LainoThis 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)I do not understand because I've used the standard procedure from PsfgenOn 11 Feb 2015 20:57, "Teodoro Laino" <teodor... at gmail.com> wrote:
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..
the fact your PSF or PDB may work with other codes means only that such codes are not performing tight checks.
Teo
On 11 Feb 2015, at 18:51, cjor <chri... at gmail.com> wrote:
Hello, I'm trying to run a QMMM simulation with CP2K based on a CHARMM FF MD simulation.
I first tried to run MM to see it works, but I get the following error:
" CP2K| version string: CP2K version 2.3 CP2K| source code revision number: 12343 CP2K| is freely available from http://www.cp2k.org/ CP2K| Program compiled at Thu Feb 28 16:12:09 GMT 2013 CP2K| Program compiled on popoca CP2K| Program compiled for Linux-x86-64-gfortran CP2K| Input file name mm.inp
GLOBAL| Force Environment number 1 GLOBAL| Basis set file name BASIS_SET GLOBAL| Geminal file name BASIS_GEMINAL GLOBAL| Potential file name POTENTIAL GLOBAL| MM Potential file name MM_POTENTIAL GLOBAL| Coordinate file name ionized.pdb GLOBAL| Method name CP2K GLOBAL| Project name phd2_md GLOBAL| Preferred FFT library FFTSG GLOBAL| Run type MD GLOBAL| All-to-all communication in single precision F GLOBAL| FFTs using library dependent lengths F GLOBAL| Global print level LOW GLOBAL| Total number of message passing processes 1 GLOBAL| Number of threads for this process 1 GLOBAL| This output is from process 0
MEMORY| system memory details [Kb] MEMORY| rank 0 min max average MEMORY| MemTotal 132089732 132089732 132089732 132089732 MEMORY| MemFree 2537384 2537384 2537384 2537384 MEMORY| Buffers 407408 407408 407408 407408 MEMORY| Cached 34948436 34948436 34948436 34948436 MEMORY| Slab 732060 732060 732060 732060 MEMORY| SReclaimable 581768 581768 581768 581768 MEMORY| MemLikelyFree 38474996 38474996 38474996 38474996
49892 0 Two molecules have been defined as identical molecules but atoms mismatch charges!! 49893 0 Two molecules have been defined as identical molecules but atoms mismatch charges!! 49894 0 Two molecules have been defined as identical molecules but atoms mismatch charges!! 49895 0 Two molecules have been defined as identical molecules but atoms mismatch charges!! 49896 0 Two molecules have been defined as identical molecules but atoms mismatch charges!! 49897 0 Two molecules have been defined as identical molecules but atoms mismatch charges!!"
I'm calling a PSF and PDF file that I know works. The error lies with the parsing of the ion section (SOD and CLA).
My MM input is:
&GLOBAL PRINT_LEVEL LOW PREFERRED_FFT_LIBRARY FFTSG PROJECT phd2_md RUN_TYPE MD&END GLOBAL
&MOTION &MD ENSEMBLE NPT_I STEPS 6000 TIMESTEP 0.48 TEMPERATURE 298.0 &THERMOSTAT TYPE NOSE REGION MASSIVE &NOSE TIMECON [wavenumber_t] 1000 &END NOSE &END THERMOSTAT &PRINT &ENERGY FILENAME =phd2_md.ener &EACH MD 1 &END EACH &END ENERGY &PROGRAM_RUN_INFO &EACH MD 1 &END EACH &END PROGRAM_RUN_INFO &END PRINT &END MD &PRINT &TRAJECTORY FILENAME =phd2_md.xyz &EACH MD 1 &END EACH &END TRAJECTORY &RESTART FILENAME =phd2_md.restart BACKUP_COPIES 1 &EACH MD 10 &END EACH &END RESTART &RESTART_HISTORY OFF &END RESTART_HISTORY &END PRINT&END MOTION
&FORCE_EVAL METHOD FIST ! Using Molecular Mechanics &MM &FORCEFIELD parm_file_name par_all27_prot_lipid.inp parmtype CHM ei_scale14 1.0 vdw_scale14 1.0 &SPLINE emax_spline 1.0 rcut_nb 12 &END SPLINE &END FORCEFIELD &POISSON &EWALD ewald_type SPME alpha 0.44 gmax 81 &END EWALD &END POISSON &END MM
&SUBSYS &CELL abc 80 80 80 periodic xyz &END CELL &KIND H BASIS_SET DZVP-GTH-BLYP POTENTIAL GTH-BLYP-q1 &END KIND &KIND O BASIS_SET DZVP-GTH-BLYP POTENTIAL GTH-BLYP-q6 &END KIND &KIND N BASIS_SET DZVP-GTH-BLYP POTENTIAL GTH-BLYP-q5 &END KIND &KIND C BASIS_SET DZVP-GTH-BLYP POTENTIAL GTH-BLYP-q4 &END KIND &KIND Fe2 BASIS_SET DZVP-MOLOPT-SR-GTH POTENTIAL DZVP-MOLOPT-SR-GTH &END KIND
&TOPOLOGY CONNECTIVITY UPSF COORDINATE PDB COORD_FILE_NAME ionized.pdb CONN_FILE_NAME ionized.psf &END TOPOLOGY &END SUBSYS&END FORCE_EVAL
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[attachment "par_all27_prot_lipid.inp" removed by Jürg Hutter/at/UZH]
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