[CP2K:6092] Topology error QMMM or MM
Teodoro Laino
teodor... at gmail.com
Thu Feb 12 21:05:00 UTC 2015
Which tone? If you believe that you have a problem with psfgen you should report this to the psfgen mailing list.
> On 12 Feb 2015, at 15:07, 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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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/ <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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