Hi all,
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>,
but there was no clear solution. The file in question is partially
written, then the seg fault always occurs during writing of the same
line/atom. I logged cpu and memory usage, but nothing strange seems to be
happening. Has anyone dealt with this problem before? Would it be
possible to use the information in sqm.out to manually create the necessary
output file? It is likely an error somewhere on my end, but I am not sure
how to go about debugging at this point and am not familiar with amber file
formats. Any suggestions would be very much appreciated.
Thanks,
Jacob
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Received on Thu May 23 2013 - 21:00:03 PDT
