> > But then multitude of lines like this shows up and program stops:
> > Info: the number of the path atoms exceeds MAXPATHATOMNUM(145000) for
> > atom[32],extend the size and reallocate the memory automatically
>
> I can confirm the problem. Antechamber runs fine if you don't ask for
> bcc charges, but gets lost in the cyclic molecule in assigning bond types
> during the bcc procedure.
>
> Not sure if any the SAMPL5 folks have run across this. I'm looking for a
> workaround, and will post anything I find here.
>
Yeah, we see this with multi-cyclic residues like CB6/CB7. Antechamber has
a maximum path length setting (see the -pl command) to help with this. Try
setting it to something like "-pl 15". My understanding is that this will
prevent antechamber from continuing to search for equivalent atoms beyond
15 bond lengths, which should be fine. As Dave indicated, without this
setting it will continue the search by circling around the molecule,
probably infinitely.
Best,
--Niel
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Received on Wed Apr 12 2017 - 10:00:03 PDT
