[CP2K-user] [CP2K:16123] Unknown element - QM/MM simulations with CP2K using AmberTools

[qingh...@gmail.com]

Providing a PDB file for your input file with a last column of element 
could possible fix your problem. 

All the best,
Qinghua

On Tuesday, October 19, 2021 at 12:28:09 AM UTC+2 isilay... at gmail.com wrote:

> I managed it this part thanks for all
>
> 18 Ekim 2021 Pazartesi tarihinde saat 23:40:30 UTC+3 itibarıyla ışılay 
> öztürk şunları yazdı:
>
>> Dear all,
>>
>> I tried to add "" <CJ>""" this unknown. ((I guess that it comes from 
>> Amber force field. I am not expert on Amber)).
>>
>> and now I have new problem 
>>
>> Possible matches for unknown subsection 
>>
>>  KIND
>>
>>    keyword MASS in section %__ROOT__%FORCE_EVAL%SUBSYS%KIND score:  106
>>    keyword POT in section %__ROOT__%FORCE_EVAL%SUBSYS%KIND score:  106
>>    keyword MAO in section %__ROOT__%FORCE_EVAL%SUBSYS%KIND score:  106
>>    subsection BS in section %__ROOT__%FORCE_EVAL%SUBSYS%KIND score:  106
>>    keyword WEIGHT in section %__ROOT__%FORCE_EVAL%SUBSYS%KIND score:  105
>>
>>
>>  *******************************************************************************
>>  *   ___                                                                  
>>      *
>>  *  /   \                                                                
>>       *
>>  * [ABORT]                                                                
>>      *
>>  *  \___/                 unknown subsection KIND of section KIND        
>>       *
>>  *    |                                                                  
>>       *
>>  *  O/|                                                                  
>>       *
>>  * /| |                                                                  
>>       *
>>  * / \                                              
>>  input/input_parsing.F:187 *
>>
>>  *******************************************************************************
>>
>>
>>  ===== Routine Calling Stack ===== 
>>
>>             5 section_vals_parse
>>             4 section_vals_parse
>>             3 section_vals_parse
>>             2 section_vals_parse
>>             1 read_input
>>
>> Please someone any idea? 
>>
>> Best wishes
>>
>> Işılay
>>
>>
>> 18 Ekim 2021 Pazartesi tarihinde saat 15:24:09 UTC+3 itibarıyla 
>> fabia... at gmail.com şunları yazdı:
>>
>>> Hi,
>>>
>>> check the &KIND section in the manual:
>>>
>>>
>>> https://manual.cp2k.org/cp2k-8_2-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/KIND.html
>>>
>>> You have to set the ELEMENT keyword.
>>>
>>> Cheers,
>>>
>>> Fabian
>>> On 17.10.2021 22:15, ışılay öztürk wrote:
>>>
>>> Dear all,
>>>
>>> I applied to forcefield with ambertools21. 
>>>
>>> When I tried to apply QMM/MM part with CP2K, I took an error message. 
>>> and that is
>>>
>>>  * [ABORT]        Unknown element for KIND <CJ>. This problem can be 
>>> fixed     *
>>>  *  \___/  specifying properly elements in PDB or specifying a KIND 
>>> section or *
>>>  *    |                getting in touch with one of  the developers!     
>>>       *
>>>  *  O/|                                                                 
>>>        *
>>>  * /| |                                                                 
>>>        *
>>>  * / \                                                   
>>>  topology_util.F:1248                                                      
>>>          *
>>>
>>> I found this page "
>>> https://docs.bioexcel.eu/qmmm_bpg/en/main/running_cp2k/cp2k_errors.html"
>>>
>>> Unfortunately, I didn't understand how I can fix it.
>>>
>>> Does someone have any idea about this?
>>>
>>> Sincerely
>>>
>>> Işılay ÖZTÜRK
>>>
>>> -- 
>>> *_______________________*
>>>
>>> *PhD. Student Işılay Öztürk*
>>>
>>> * EGE UNIVERSITY  Graduate School of Natural and Applied Science 
>>> Departmant of Chemistry / Physical Chemistry 35100 Bornova / IZMIR / TURKEY 
>>> *
>>>
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>>> .
>>>
>>>

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