Yes, the crash does indeed happen on the index of the (single) CLA
ion.
No, I am not interested in GB calculations at the moment. I suppose I
can happily use the current top file with all the GB radii set to
zero. But it's still a bug and I don't have problems with other PSFs
which contain hundreds of ions.
The mangled string (I think it was just all NULs) obviously came from
radius_set_name not being set because get_gbradii wasn't called.
Thanks for your reply,
Hannes.
On Wed, 18 Jan 2012 09:02:00 -0500
Jason Swails <jason.swails.gmail.com> wrote:
> Does gdb tell you what the value of "i" is at that point in the
> loop? I'm wondering if it's a free ion and no bonded partners
> exist... In this case, you wouldn't want to run GB calculations,
> anyway, right?
>
> (Also, what string is mangled?).
>
> All the best,
> Jason
>
> On Wed, Jan 18, 2012 at 5:44 AM, Hannes Loeffler
> <Hannes.Loeffler.stfc.ac.uk
> > wrote:
>
> > Hi,
> >
> > chamber from the AmberTools 1.5 segfaults on one of my PSF files.
> >
> > Last output:
> >
> > --- Found all ATOM TYPES in topology file
> >
> > Gdb tells me
> >
> > Program received signal SIGSEGV, Segmentation fault.
> > 0x0807880f in get_gbradii (rs=2) at _gbradii.f:91
> > 91 currently_bonded_atom = element
> > ( locattype( bonded_list(1, i) ) )
> >
> > Commenting out the call to get_gbradii in psfprm.f produces the
> > output files as expected except for the missing GB radii in the top
> > file (and a mangled string just above %FLAG RADII).
> >
> >
> > Thanks,
> > Hannes
> > --
> > Scanned by iCritical.
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
--
Scanned by iCritical.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 18 2012 - 07:00:03 PST
