[CP2K-user] [CP2K:14868] Restart with atom kind error

[Amami Haruka]

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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