ERROR in check_subsys_element (MODULE topology_util)

jadefox337 jadef... at
Mon Aug 15 22:22:11 UTC 2011


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,


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