Dear Jacob,
> 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.
splitting a conjugated system into different building blocks is more tricky...
difficult to help without a picture of your molecule...
regards, Francois
> 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.
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Received on Sat May 25 2013 - 09:30:03 PDT
