[CP2K-user] [CP2K:16691] CP2K bug while reading a cif file from COD

Mozhdeh Mohammadpour mozhdehmohammadpour at gmail.com
Thu Mar 10 09:36:15 UTC 2022

Hi CP2K experts, 

I am using COD cif files for some polymorphs of glycine. However, It seems 
that CP2K has some issues with reading gamma glycine 
I suppose it might be a problem with the cif file, but CP2K starts to write 
a warning infinite times:

 GENERATE|  Preliminary Number of Bonds generated:                         

 GENERATE| WARNING in connectivity generation!
 GENERATE| Two molecules/residues named (MOL2) have different  number of 
 GENERATE| Molecule starting at position (12) has Nr. <0> of atoms.
 GENERATE| while the other same molecules have Nr. <1> of atoms!
 GENERATE| Increasing bondparm_factor by 1.05.. An error was found in the 
 GENERATE| connectivity. Retry...
 GENERATE| Present value of BONDPARM_FACTOR (   Infinity ).

and the output file size goes up to Gigabytes in a few seconds. 

Apologies if I wrote 'bug' and it is not. I appreciate any help on this. 

Kindest regards,

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