I only ran as part of antechamber. I don't think sqm is having the issue,
since it is producing a complete sqm.out file. Looking at other
antechamber output, I was able to manually build the final files with the
information in sqm.out, which, I am embarrassed to say, should have been
much more obvious at first. If I understand the process behind
antechamber, the segfault seems to occur while running the code for am1bcc
or possibly antechamber itself when the file ANTECHAMBER_AM1BCC_PRE.AC is
being written. Looking at the source code, I'm not exactly sure where this
is. One could turn on debugging, recompile, and try and pinpoint the
error, but since I have a solution I am not sure that this would be the
best use of my time. I can send all of my input files and command line
options if you like, but this seems to be only a minor issue affecting a
small number of people. Again, thank you for your help.
Best,
Jacob
On Sat, May 25, 2013 at 8:30 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Fri, May 24, 2013, Jacob Monroe wrote:
> >
> > 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.
>
> As with the earlier case, your file works fine for me. Did you run sqm by
> itself, or only as a part of antechamber? Best advice beyond that is to
> upgrade to the current version, which is two releases beyond what you have.
>
> ...dac
>
>
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Received on Mon May 27 2013 - 09:30:03 PDT
