Francois and David,
Thank you both very much for your suggestions. Francois, looking at the
links you provided, I will certainly investigate different ways of
parameterizing the molecule in representative units. I was hesitant to do
this at first since the molecule contains an extended network of aromatic
rings linked by oxygen atoms, but agree that it is certainly worth looking
into.
I have amber11 with AmberTools 1.4 installed on CentOS. I have not had any
trouble with any other molecules, only this one. The sqm.in file is
attached if you would like to try and reproduce the error. Again, thank
you for your advice and time.
Best,
Jacob
On Fri, May 24, 2013 at 8:11 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, May 23, 2013, Jacob Monroe wrote:
> >
> > When I run antechamber for a specific molecule, it throws a seg fault
> after
> > sqm finishes. The molecule is large at 184 atoms, and has a -8 charge,
> but
> > this should not be an issue once calculations are completed. A similar
> > problem was mentioned in the
> > archive<http://archive.ambermd.org/201101/0383.html>,
>
> Note that in the archive article you mention, I could not reproduce the
> problem. This suggests that we need information about which version you
> are
> using, and which OS and compiler are involved.
>
> If you wish, you can post the sqm.in file, and I'll try to run it here. It
> could be that this time the error will be reproducible. If not, you'll
> have
> to compile sqm with debug options and run it under the debugger to try to
> find
> the source of the error.
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/octet-stream attachment: sqm.in
Received on Fri May 24 2013 - 13:30:02 PDT
