AMBER Archive (2004)

Subject: RE: AMBER: ambpdb segmentation fault

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Nov 17 2004 - 15:35:40 CST

Hi Justin,

I have tried this out on our G5 and can't reproduce the problem you are
seeing. We are using xlf90 v8.1. I have attached the config.h file I used
for this. Try using this instead of your config.h file. Make sure you do
"make clean" in $AMBERHOME/src before recompiling.

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of justin litchfield
> Sent: 15 November 2004 18:57
> To: amber_at_scripps.edu
> Subject: AMBER: ambpdb segmentation fault
>
> I've just recently installed amber8 on a G5 powermac (dual 1.8GHz),
> which seems to have worked fine. all the modules i've used so far
> (nucgen, sander, xleap) work fine, but while working through
> the first
> DNA tutorial, i found that ambpdb returns a segmentation fault every
> time i call it, regardless of the input (even none). this is
> the input
> i was trying to get to work:
>
> ambpdb -p polyAT_vac.prmtop < polyAT_vac_init_min.rst >
> polyAT_vac_init_min.pdb
>
> and i made sure that the input files were all valid, matched the
> tutorial, etc.
>
> i applied the patch bugfix.all and recompiled, and am now at
> a loss as
> to what to do. i'm really new to unix systems and compiling and
> whatnot, so your help is definitely appreciated. thanks,
>
> justin litchfield
>
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