[CP2K:10351] Novel atom types in CHARMM force field - QM/MM MD case

Rizwan Nabi rizwan... at gmail.com
Wed May 30 23:30:19 UTC 2018

Dear David
You have to mention basis sets for O atoms as well in the &KIND section of

On Thu, 31 May 2018, 00:48 'Dawid das' via cp2k, <cp... at googlegroups.com>

> Dear CP2K Users,
> I am completely new to CP2K and I would like to perform QM/MM molecular
> dynamics simulation of protein
> solvated in a box of water with counterions (system is neutral).
> I would like to do it at the B3LYP/GPAW or B3LYP/GPW level of theory for
> QM subsystem and CHARMM22
> force field for classical part. I use link atoms approach, PBC (at least
> for electrostatics in classical part,
> I don't know how about the QM part yet) and electrostatic embedding. I
> think these are the most important
> points of what I want to do.
> I went through exemplary inputs for QM/MM MD simulations I could find on
> this group and on CP2K website
> and there is one thing however I cannot overcome but I think I know the
> source of issue.
> My protein is a fluorescent protein and I have definition of non-standard
> atom types in my CHARMM force
> field.
> At the end of the log I get following error:
>  ****************************************************
>  *** ERROR in read_qs_kind (MODULE qs_kind_types) ***
>  ****************************************************
>  *** No &KIND section was possible to associate to the atomic kind <O>.
> ***
>  *** The KIND section were also scanned for the corresponding element <O>
> ***
>  *** and for the DEFAULT section but no match was found. Check your input
> ***
>  *** file!
> ***
>  *** Program stopped at line number 1840 of MODULE qs_kind_types ***
> I don't really know how to proceed further...
> I guess CP2K cannot recognize correctly MO3, MOH, MN3, etc. types as
> oxygen, nitrogen, etc.
> I tried to play with &KIND section but I'm not really sure how to make it
> to make sense.
> I attach my input  files and I will be grateful for any explanations. The
> QM subsystem is for
> now very small as I just want to start off a simulation to check whether
> it works or not.
> Best wishes,
> Dawid Grabarek
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