Topology error QMMM or MM

[cjor]

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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