New atom types and topology/parameter files

[Ghazaleh Zm]

Dear Christoph

I‌ had similar problem as yours recently. 
In your version 1 input file, you defined Kind A1, Kind A2, Kind A3, while 
in your PSF file these are atom names and the atom types are A, A, and B 
(the next tab). 
Therefore you should define Kind A and Kind B in the input file. 

I hope it helps you. 

Ghazaleh 

On Monday, June 26, 2017 at 9:04:26 PM UTC+2, Christoph wrote:
>
> Dear CP2K users,
>
> I would simulate on the MM level an artificial test system with CP2K 
> (artificial refering here to the atom types), using CHARMM 
> topology/parameter files.
>
> As a minimal example, I have prepared a geometry optimization for a 
> 3-atomic molecule, which I fail to get working for MM only simulations. The 
> input files for two versions, 1 and 2, are attached.
>
> When running version 1 I get:
>
>
>
>  *******************************************************************************
>  *   ___                                                                   
>     *
>  *  /   \                                                                 
>      *
>  * [ABORT]  Unknown element for KIND <A>. 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:1271 *
>
>  *******************************************************************************
>
>
>  ===== Routine Calling Stack ===== 
>
>             6 connectivity_control_check_element_name
>             5 connectivity_control
>             4 topology_control
>             3 fist_init
>             2 fist_create_force_env
>             1 CP2K
>
> Program received signal SIGABRT: Process abort signal.
>
> Backtrace for this error:
> #0  0x23458CD in _gfortrani_backtrace at backtrace.c:258
> #1  0x2320A20 in _gfortrani_backtrace_handler at compile_options.c:129
> #2  0x42DE5F in _L_unlock_13 at funlockfile.c:?
> #3  0x42DD2B in raise at pt-raise.c:37
> #4  0x23BF037 in abort at abort.c:78
> #5  0x1E20288 in __message_passing_MOD_mp_abort at message_passing.F:1034
> #6  0x1E74B87 in __base_hooks_MOD_cp_abort at base_hooks.F:68
> #7  0xF33EE6 in __topology_util_MOD_check_subsys_element at 
> topology_util.F:1275 (discriminator 15)
> #8  0xC2AE9A in __topology_MOD_connectivity_control at topology.F:355
> #9  0xC2BBEC in __topology_MOD_topology_control at topology.F:187
> #10  0x7B561B in __cp_subsys_methods_MOD_cp_subsys_create at 
> cp_subsys_methods.F:152
> #11  0x141C867 in __fist_environment_MOD_fist_init at 
> fist_environment.F:161
> #12  0x137345F in __fist_main_MOD_fist_create_force_env at fist_main.F:97
> #13  0xBA17C1 in __f77_interface_MOD_create_force_env at 
> f77_interface.F:752
> #14  0x437116 in __cp2k_runs_MOD_cp2k_run at cp2k_runs.F:276
> #15  0x43AA9C in __cp2k_runs_MOD_run_input at cp2k_runs.F:1099
> #16  0x4301DE in MAIN__ at cp2k.F:281
>
>
>
> I guess one cannot specify new element types in CP2K via the input files 
> only. In version 2 of my example files the atom type is changed to "C" 
> (both in the PDB and the CP2K KIND input files), which should be known by 
> CP2K. However, I get with when running version 2:
>
>
>  *******************************************************************************
>  *   ___                                                                   
>     *
>  *  /   \                                                                 
>      *
>  * [ABORT]                                                                 
>     *
>  *  \___/       A string type object was expected, found end of line, 
> File:    *
>  *    |                    '../system1.prm', Line: 13, Column: 6           
>     *
>  *  O/|                                                                   
>      *
>  * /| |                                                                   
>      *
>  * / \                                         
>  input/cp_parser_methods.F:1253 *
>
>  *******************************************************************************
>
>
>  ===== Routine Calling Stack ===== 
>
>             5 read_force_field_charmm
>             4 force_field_control
>             3 fist_init
>             2 fist_create_force_env
>             1 CP2K
>
> Program received signal SIGABRT: Process abort signal.
>
> Backtrace for this error:
> #0  0x23458CD in _gfortrani_backtrace at backtrace.c:258
> #1  0x2320A20 in _gfortrani_backtrace_handler at compile_options.c:129
> #2  0x42DE5F in _L_unlock_13 at funlockfile.c:?
> #3  0x42DD2B in raise at pt-raise.c:37
> #4  0x23BF037 in abort at abort.c:78
> #5  0x1E20288 in __message_passing_MOD_mp_abort at message_passing.F:1034
> #6  0x1E74B87 in __base_hooks_MOD_cp_abort at base_hooks.F:68
> #7  0x19C149C in __cp_parser_methods_MOD_parser_get_string at 
> cp_parser_methods.F:1255 (discriminator 2)
> #8  0x15789FF in __force_fields_ext_MOD_read_force_field_charmm at 
> force_fields_ext.F:434
> #9  0x141D28D in __force_fields_MOD_force_field_control at 
> force_fields.F:158
> #10  0x141C90C in __fist_environment_MOD_fist_init at 
> fist_environment.F:169
> #11  0x137345F in __fist_main_MOD_fist_create_force_env at fist_main.F:97
> #12  0xBA17C1 in __f77_interface_MOD_create_force_env at 
> f77_interface.F:752
> #13  0x437116 in __cp2k_runs_MOD_cp2k_run at cp2k_runs.F:276
> #14  0x43AA9C in __cp2k_runs_MOD_run_input at cp2k_runs.F:1099
> #15  0x4301DE in MAIN__ at cp2k.F:281
> /home/jadzia/Dropbox/Software/installed/bin/cp2k: line 5:  2732 Aborted   
>               ${script_dir}/cp2k.ssmp $@
>
>
>
> If possible I would like to get this working with them CHARMM files rather 
> than with CP2K keywords. I know that there are other programs which are 
> specialized on MM simulations, but I want to use CP2K due to some special 
> features it has. 
>
> Looking forward to your comments.
>
> Best wishes,
> Christoph
>
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