[CP2K-user] [CP2K:18619] Topology generating error

[Xianyuan Zhao]

Dear cp2k experts,

I'm trying to set up a simulation small box with 22 water and 7 Li+ and 
7Br-.  I generated my initial configuration with Packmol and adjusted in 
VMD to avoid atom overlapping in periodic boundary condition (graph 
attached).  Seems there is some error when generating topology for Li which 
should be easy to generate since they are not bonded at all!  I defined 
KIND in SUBSYS section and tried to set their COVALENT_RADIUS to 0.  My 
input file is attached.

The error message I got is as following

 GENERATE|  Preliminary Number of Bonds generated:                         
   44

 GENERATE| WARNING in connectivity generation!
 GENERATE| Two molecules/residues named (Li) have different  number of 
atoms.
 GENERATE| Molecule starting at position (68) has Nr. <0> of atoms.
 GENERATE| while the other same molecules have Nr. <2> of atoms!
 GENERATE| Increasing bondparm_factor by 1.05.. An error was found in the 
generated
 GENERATE| connectivity. Retry...
 GENERATE| Present value of BONDPARM_FACTOR (   1.155000 ).


 GENERATE|  Preliminary Number of Bonds generated:                         
   44

 GENERATE| WARNING in connectivity generation!
 GENERATE| Two molecules/residues named (Li) have different  number of 
atoms.
 GENERATE| Molecule starting at position (68) has Nr. <0> of atoms.
 GENERATE| while the other same molecules have Nr. <2> of atoms!
 GENERATE| Increasing bondparm_factor by 1.05.. An error was found in the 
generated
 GENERATE| connectivity. Retry...
 GENERATE| Present value of BONDPARM_FACTOR (   1.212750 ).


I've also tried using input COORD_FILE_NAME and CONN_FILE_NAME with pdb and 
psf, respectively.  But it seems this approach didn't work either.  There 
was no output at all.  I also attache the pdb and psf files to this message.

Please help me identify the problem.

Thank you very much!

Regards,

Xianyuan

[image: Screenshot 2023-04-05 175210.png]

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