Unknown element - QM/MM simulations with CP2K using AmberTools

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ışılay öztürk

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Oct 17, 2021, 4:16:04 PMOct 17
to cp...@googlegroups.com
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                                                               *


Unfortunately, I didn't understand how I can fix it.

Does someone have any idea about this?

Sincerely

Işılay ÖZTÜRK

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PhD. Student Işılay Öztürk

EGE UNIVERSITY 
Graduate School of Natural and Applied Science
Departmant of Chemistry / Physical Chemistry
35100 Bornova / IZMIR / TURKEY

Fabian Ducry

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Oct 18, 2021, 8:24:09 AMOct 18
to cp...@googlegroups.com

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

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ışılay öztürk

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Oct 18, 2021, 4:40:30 PMOct 18
to cp2k
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...@gmail.com şunları yazdı:

ışılay öztürk

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Oct 18, 2021, 6:28:09 PMOct 18
to cp2k
I managed it this part thanks for all

18 Ekim 2021 Pazartesi tarihinde saat 23:40:30 UTC+3 itibarıyla ışılay öztürk şunları yazdı:

qingh...@gmail.com

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Oct 26, 2021, 8:29:07 AMOct 26
to cp2k
Providing a PDB file for your input file with a last column of element could possible fix your problem.

All the best,
Qinghua
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