[CP2K:4545] error in reading amber topology

Teodoro Laino teodor... at gmail.com
Sat Aug 10 17:48:43 CEST 2013


check that your PDB contains the element field (column 77-78). If you'll provide the element in the PDB, cp2k will not have try to guess the element from the atom name/type.

=> cp2k may rename the types - this could justify why you do not have any HX in your files. There are reasons for renaming - check old posts for the reason.


On Aug 10, 2013, at 5:08 PM, Geoffrey Wood <ge.f... at gmail.com> wrote:

> Dear Forum,
> 
> I am reading in an amber topology created by tleap (with the corresponding pdb file created by tleap) but I am getting this error in cp2k (I have no HX's in either of them)?  Does any one know what this is about?
> 
> Thanks.
> 
>  ************************************************************
>  *** ERROR in check_subsys_element (MODULE topology_util) ***
>  ************************************************************
> 
>  ***  Unknown element for KIND <HX>. This problem can be fixed specifying ***
>  *** properly elements in PDB or specifying a KIND section or getting in  ***
>  *** touch with one of  the developers!                                   ***
> 
>  *** Program stopped at line number 1371 of MODULE topology_util ***
> 
>  ===== Routine Calling Stack ===== 
> 
>             7 connectivity_control_check_element_name
>             6 connectivity_control
>             5 topology_control
>             4 fist_init
>             3 fist_create_force_env
>             2 qmmm_create_force_env
>             1 CP2K
> 
> 
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