ERROR in check_subsys_element (MODULE topology_util)

[jadefox337]

Unfortunately, this is not the problem.  The element is specified
correctly as H and no other control characters appear in the file.

On Aug 16, 12:05 am, Teodoro Laino <teodor... at gmail.com> wrote:
> The error is pretty clear: what you have introduced, is interpreted as element "59". Clearly this is not a known element.
> Why that? your fault in formatting PDB, PSF or specifying 59 in the XYZ.
> If you really want a type called 59 then  you need to specify what kind of element it is.
>
> Check carefully your input files.
> Teo
>
> On Aug 16, 2011, at 12:22 AM, jadefox337 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
>
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>