New atom types and topology/parameter files
Christoph
c.gor... at gmail.com
Tue Jun 27 11:43:26 UTC 2017
Dear Ghazaleh,
Thank you very much for your helpful answer.
Your suggestion seems to work indeed if in addition I change the element
type to one of the known elements. (Also, I found that in the attached
CHARMM paramter input file the DIHEDRALS keyword was incorrect.)
Best wishes,
Christoph
On Tuesday, June 27, 2017 at 6:17:57 AM UTC-4, Ghazaleh Zm wrote:
>
> 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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