FIST: BONDS, Angles from PSF: Old BOND Count, New BOND Count.

ganta.pra... at gmail.com ganta.pra... at gmail.com
Fri Nov 3 20:41:27 CET 2017


Dear CP2K team/users,


When I import PSF file, CP2K reads everything fine but after reading PSF 
file, CP2K generate bonds and angles and .... (don't know why). I have 
switched off GENERATE too. 

 
I have even dumped PSF from CP2K and compared with my PSF.  In both PSFs, I 
have 384 bonds (correct number of bonds). But when CP2K is running it says 
64 bonds. 


For instance, in the output file: When CP2K reads my PSF, the output is:

   Mol(           1 ) Old BOND Count:          348           3         

then, the output is updated saying

  Mol(           1 ) New BOND Count:           64           1  


Attached are my input file, output file and psf pdb files. Due to missing 
bonds, I am having errors and I got NaN energies (I think). 

Please let me know if you have any suggestions. 

Regards,
Prasanth. 

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