ERROR in check_subsys_element (MODULE topology_util)

[jadefox337]

One more detail: I have tried various configuration of my input and
sometimes the *btr file created contains the following:


cp2k.popt_2.2.163:31074 terminated with signal 11 at PC=117df9a
SP=7fff73ac6dd0.  Backtrace:
/modfac/bin/cp2k.popt_2.2.163(cp_fm_diag_mp_cp_fm_syevd_+0xa1a)
[0x117df9a]
/modfac/bin/cp2k.popt_2.2.163[0x101c564]
/modfac/bin/cp2k.popt_2.2.163(geo_opt_mp_cp_geo_opt_+0x4c1)[0x5ce0d1]
/modfac/bin/cp2k.popt_2.2.163(cp2k_runs_mp_run_input_+0x1773)
[0x4bc633]
/modfac/bin/cp2k.popt_2.2.163(MAIN__+0x1025)[0x4b7565]
/modfac/bin/cp2k.popt_2.2.163(main+0x3c)[0x4b652c]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x325ee1d994]
/modfac/bin/cp2k.popt_2.2.163[0x4b6439]


On Aug 15, 3:22 pm, jadefox337 <jadef... at gmail.com> wrote:
> Hello,
>
> I am running a standard geometric optimization, except that I am
> placing an optimized group of HCl + 4 water on a sugar.  The optimized
> group is in fact ionized HCl that turned into Hydronium+, Cl- and some
> water.  The program fails with the following  (where 59 is the index
> of the H of the original HCl and which is now connected to a water):
> __________________
>
>  ************************************************************
>  *** ERROR in check_subsys_element (MODULE topology_util) ***
>  ************************************************************
>
>  ***  Unknown element for KIND <59>. This problem can be fixed
> specifying ***
>  *** properly elements in PDB or specifying a KIND section or getting
> in  ***
>  *** touch with one of  the
> developers!                                   ***
> __________________________________________
>
> Does anyone have any idea how to fix this problem without actually
> moving the H near the Cl (which by the way I did already, and caused
> to crash without error explanation - some *btd files were created).
>
> I can supply input if needed.
>
> Thanks much,
>
> Madeleine