[CP2K:6150] Topology error QMMM or MM
Christian Jorgensen
chri... at gmail.com
Thu Feb 12 20:15:56 UTC 2015
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 on
> this 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 NA
>> ATOM 49881 SOD SOD I 38 24.667 -35.051 19.114 1.00 0.00
>> ION NA
>> ATOM 49882 SOD SOD I 39 -12.620 2.426 26.969 1.00 0.00
>> ION NA
>> ATOM 49883 SOD SOD I 40 -10.705 -33.380 -11.158 1.00 0.00
>> ION NA
>> ATOM 49884 SOD SOD I 41 -19.491 29.350 -34.679 1.00 0.00
>> ION NA
>> ATOM 49885 SOD SOD I 42 40.802 -30.866 10.911 1.00 0.00
>> ION NA
>> ATOM 49886 SOD SOD I 43 -21.411 -20.389 17.270 1.00 0.00
>> ION NA
>> ATOM 49887 SOD SOD I 44 13.100 24.287 18.857 1.00 0.00
>> ION NA
>> ATOM 49888 SOD SOD I 45 33.628 30.716 18.333 1.00 0.00
>> ION NA
>> ATOM 49889 SOD SOD I 46 14.256 -31.556 -9.097 1.00 0.00
>> ION NA
>> ATOM 49890 SOD SOD I 47 -1.600 38.825 28.079 1.00 0.00
>> ION NA
>> ATOM 49891 SOD SOD I 48 26.911 -9.319 19.217 1.00 0.00
>> ION NA
>> ATOM 49892 CLA CLA I 49 -21.849 -29.233 -4.389 1.00 0.00
>> ION CL
>> ATOM 49893 CLA CLA I 50 -27.778 19.207 -8.907 1.00 0.00
>> ION CL
>> ATOM 49894 CLA CLA I 51 -1.036 -18.525 -33.557 1.00 0.00
>> ION CL
>> ATOM 49895 CLA CLA I 52 -37.955 23.751 -9.529 1.00 0.00
>> ION CL
>> ATOM 49896 CLA CLA I 53 -15.636 -34.005 12.873 1.00 0.00
>> ION CL
>> ATOM 49897 CLA CLA I 54 40.122 21.296 -26.349 1.00 0.00
>> ION CL
>> ATOM 49898 CLA CLA I 55 32.593 -9.101 17.836 1.00 0.00
>> ION CL
>> ATOM 49899 CLA CLA I 56 8.168 -24.215 8.246 1.00 0.00
>> ION CL
>> ATOM 49900 CLA CLA I 57 -4.530 -32.691 -6.031 1.00 0.00
>> ION CL
>> ATOM 49901 CLA CLA I 58 -14.998 37.422 2.603 1.00 0.00
>> ION CL
>> ATOM 49902 CLA CLA I 59 -22.559 -24.866 -37.160 1.00 0.00
>> ION CL
>> ATOM 49903 CLA CLA I 60 22.442 -17.653 -37.184 1.00 0.00
>> ION CL
>> ATOM 49904 CLA CLA I 61 -31.657 0.756 -22.411 1.00 0.00
>> ION CL
>> ATOM 49905 CLA CLA I 62 -25.707 4.569 26.200 1.00 0.00
>> ION CL
>> ATOM 49906 CLA CLA I 63 9.816 21.844 -29.523 1.00 0.00
>> ION CL
>> ATOM 49907 CLA CLA I 64 20.348 15.655 31.373 1.00 0.00
>> ION CL
>> ATOM 49908 CLA CLA I 65 -33.471 28.927 25.816 1.00 0.00
>> ION CL
>> ATOM 49909 CLA CLA I 66 -23.076 -36.320 -14.581 1.00 0.00
>> ION CL
>> ATOM 49910 CLA CLA I 67 11.228 23.055 26.442 1.00 0.00
>> ION CL
>> ATOM 49911 CLA CLA I 68 -31.967 -25.220 12.122 1.00 0.00
>> ION CL
>> ATOM 49912 CLA CLA I 69 7.122 -32.163 -23.902 1.00 0.00
>> ION CL
>> ATOM 49913 CLA CLA I 70 -30.542 -17.921 15.502 1.00 0.00
>> ION CL
>> ATOM 49914 CLA CLA I 71 -35.163 -32.044 11.857 1.00 0.00
>> ION CL
>> ATOM 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 written
>> for VMD.
>>
>>
>>
>>
>>
>>
>>
>>
>> On Wed, Feb 11, 2015 at 9:14 PM, Christian Jorgensen <chri... at gmail.com
>> > wrote:
>>
>>> Hello Dr Laino
>>>
>>> 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)
>>>
>>> I do not understand because I've used the standard procedure from Psfgen
>>> On 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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>>>
>>
>>
>> --
>> _______
>>
>> Christian Jørgensen
>>
>> --
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>
>
>
> --
> _______
>
> Christian Jørgensen
>
--
_______
Christian Jørgensen
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