[CP2K:3429] ERROR in check_subsys_element (MODULE topology_util)

Teodoro Laino teodor... at gmail.com
Tue Aug 16 07:05:19 UTC 2011

The error is pretty clear: what you have introduced, is interpreted as element "59". Clearly this is not a known element.
Why that? your fault in formatting PDB, PSF or specifying 59 in the XYZ.
If you really want a type called 59 then  you need to specify what kind of element it is.

Check carefully your input files.

On Aug 16, 2011, at 12:22 AM, jadefox337 wrote:

> Hello,
> I am running a standard geometric optimization, except that I am
> placing an optimized group of HCl + 4 water on a sugar.  The optimized
> group is in fact ionized HCl that turned into Hydronium+, Cl- and some
> water.  The program fails with the following  (where 59 is the index
> of the H of the original HCl and which is now connected to a water):
> __________________
> ************************************************************
> *** ERROR in check_subsys_element (MODULE topology_util) ***
> ************************************************************
> ***  Unknown element for KIND <59>. This problem can be fixed
> specifying ***
> *** properly elements in PDB or specifying a KIND section or getting
> in  ***
> *** touch with one of  the
> developers!                                   ***
> __________________________________________
> Does anyone have any idea how to fix this problem without actually
> moving the H near the Cl (which by the way I did already, and caused
> to crash without error explanation - some *btd files were created).
> I can supply input if needed.
> Thanks much,
> Madeleine
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