[CP2K:3432] Re: ERROR in check_subsys_element (MODULE topology_util)

[Teodoro Laino]

please post all your input files then..

On Aug 16, 2011, at 9:59 PM, jadefox337 wrote:

> Unfortunately, this is not the problem.  The element is specified
> correctly as H and no other control characters appear in the file.
> 
> On Aug 16, 12:05 am, Teodoro Laino <teodor... at gmail.com> wrote:
>> 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.
>> Teo
>> 
>> 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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>> 
>> 
> 
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