[CP2K:6097] Topology error QMMM or MM
luca
lcb... at gmail.com
Fri Feb 13 11:01:24 UTC 2015
Hi Christian
it is just a suggestion, but, you can improve your chances to resolve
this kind of problem, providing a simpler system that is able reproduce
the error. (ther is
>From your output seems that the problem arise from the ions atoms;
so, why do you not test two small systems? one composed by 10 water
molecules with 1 SOD + 1 CLA and another system without ions.
In this way you can provide small and simple input files that you and
and the developers can easily check!
Maybe, you can solve it alone.
The system without SOD and CLA should work!
Good luck,
Luca
> My apologies. I've reported it now.
>
>
> On 12 Feb 2015 21:47, "Teodoro Laino" <teodor... at gmail.com> wrote:
> 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> 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
> >
> >
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