On Mon, Mar 24, 2014, Hannes Loeffler wrote:
>
> I just realised where the actual problems is. Leap does a valency
> check by default and refuses to accept more than one bond per hydrogen.
> It will keep the very first bond it encounters in the input and discard
> others that may have been defined. I have overlooked this and
> accidentally created the same bond twice (after set pert true).
>
> I wonder though why leap would allow this when this will result in a
> fatal error on parmtop writing anyway. Is there a valid use case for
> this or shouldn't this better be captured at the time a user tries to
> create the same bond again?
Can you (re-)send a test case that shows the problem, based on your recent
understanding of what is happening? I think the "pert" flag in LEaP is no
longer relevant, and should never be set, and we might not be catching errors
that involve its use. But it's not clear whether or not "pert" is involved
in your problem or not.
Thanks for sending these reports, and for finally finding the cause of the
original problem.
...regards...dac
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Received on Tue Mar 25 2014 - 07:00:03 PDT
