[CP2K-user] [CP2K:14871] Restart with atom kind error

[Amami Haruka]

adding the missing atoms seems to give another problem.
The original simulation runs fine for a very long time. 
cp2k.psmp equil.inp > equil.out
However, restart the simulation with the same file gives
cp2k.psmp test.inp > test.out

  Translating the system in order to center the QM fragment in the QM box.

 *******************************************************************************
 *   ___                                                                       *
 *  /   \                                                                      *
 * [ABORT]                                                                     *
 *  \___/                             CPASSERT failed                          *
 *    |                                                                        *
 *  O/|                                                                        *
 * /| |                                                                        *
 * / \                                                  cp_ddapc_methods.F:652 *
 *******************************************************************************


 ===== Routine Calling Stack ===== 

            9 ewald_ddapc_pot
            8 cp_ddapc_create
            7 cp_ddapc_init
            6 qs_env_update_s_mstruct
            5 qs_energies_init_hamiltonians
            4 qs_energies
            3 qs_forces
            2 qs_mol_dyn_low
            1 CP2K




> On 3 Mar 2021, at 20:58, Amami Haruka <amami... at gmail.com> wrote:
> 
> Ok, I solved the problem.
> If your input file has an unusual atom mapping. For example, a proton in your ligand has atom name HX.
> cp2k could only recognise this mapping from HX to H, if both the topology file and coordinate file are provided.
> 
> So you would need
> 
>     &TOPOLOGY
>       CONN_FILE_FORMAT AMBER
>       CONN_FILE_NAME MM.prmtop
>       COORD_FILE_NAME npt.pdb
>       COORD_FILE_FORMAT PDB
>     &END TOPOLOGY
> 
> and this won't work.
> 
>     &TOPOLOGY
>       CONN_FILE_FORMAT AMBER
>       CONN_FILE_NAME MM.prmtop
>     &END TOPOLOGY
> 
> Given that the amber topology contains this mapping information, I think it would be more useful if the cp2k could read this mapping information when only CONN_FILE is provided.
> In cp2k-8.1/src/topology_util.F, SUBROUTINE check_subsys_element(element_in, atom_name_in, element_out, subsys_section, use_mm_map_first) doesn't seems to do this.
> 
> On Wednesday, 3 March 2021 at 15:45:41 UTC Amami Haruka wrote:
> Sorry, there seems to be a problem with attaching files.
> 
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