On Fri, 11 Jul 2014 08:16:55 -0700
Jason Swails <jason.swails.gmail.com> wrote:
>
> On Jul 11, 2014, at 1:41 AM, Sushil Mishra <sushilbioinfo.gmail.com>
> wrote:
>
> > Dear all,
> >
> > Has someone tried to debug this issue ? I have the same issue under
> > ubuntu 12.04 in x86_64 HP workstation. It works fine on the
> > structure dummy atoms. If someone would like to reproduce the
> > problem, there is a structure attached herewith.
>
> I can confirm that parmchk2 segfaults for me as well on my Linux
> machine. However, "parmchk" works just fine, and in this case is
> functionally equivalent to parmchk2 (since no parameters can be
> found, anyway). It works fine on my Mac.
>
> In the meantime I'll look into the segfault.
I have tried to run this with gdb and gdb thinks the segfaults happens
in line 1618 of parmchk2.c . The problem apparently is the variable
pid used in this line for indexing which evaluates to -1 for unknown
atom types. That's the preset value in assign_parmid() (lines
1404ff). I guess the numbers in parmid are bcc types.
Cheers,
Hannes.
--
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Received on Thu Jul 24 2014 - 08:00:02 PDT
