[CP2K-user] New KIND generated after minimization

[qi...@gmail.com]

Hello,

I am running QM/MM MD simulations using CP2K 7.1. I found that I could not 
do the minimization starting from a CRD (rst) file, but it could be done 
starting from a PDB file,
which was generated with amb2pdb from Amber.
The error reported is: 
#
Unknown element for KIND <NG>. This problem can be fixed 
specifying properly elements in PDB or specifying a KIND section or 
getting in touch with one of  the developers! 
#
I checked my system, I did not find an atom named NG.

Even though the minimization was done successfully starting from a PDB 
file, but the subsequent NVT equilibration was failed due to the same 
error. After I added a section of
NG (I assume it is nitrogen), the NVT equilibration was running 
successfully. 

Is there a way to convert the restart file into a pdb file, so that I can 
check which atom was renamed to NG by CP2K? Any suggestion? Thanks a lot!
 
All the best,
Qinghua
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20210202/ada434bb/attachment.htm>