Hi again,
On Fri, 11 Oct 2013 17:18:43 +0100
Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
> Hi,
>
> I found a problem with leap handling dummy atoms when it is in the
> middle of the atom sequence as in the attached example (test.mol2).
> Looks like a bug to me.
>
> For the hydrogen bonded to it pert is set to true and the bond between
> the two recreated. Leap terminates with the following message.
>
> !FATAL ERROR----------------------------------------
> !FATAL: In file [unitio.c], line 1805
> !FATAL: Message: 1-4: cannot add bond 7 8
> This may be caused by duplicate bond specifications;
> for example, explicit bond commands in addition to PDB conect records.
> !
> !ABORTING.
>
> When the dummy is pushed to the end of the sequence as in test2.mol2
> leap runs fine with the mol2 and the created parm file looks ok.
>
> The attachment contains a leap script leap.in to built the output
> files.
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?
Cheers,
Hannes.
--
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Received on Mon Mar 24 2014 - 05:30:03 PDT
