Hi,
On Wed, Jan 11, 2023 at 10:30 AM Thorben Poburski via AMBER
<amber.ambermd.org> wrote:
> 0: [xtalsymm :1-124,128-251,255-378,382-505,509-632,636-759 group
> 'P3(2)21' collect centroid first]
> ----- rnasea_unitcell4025.inpcrd (1-1, 1) -----
> j = 0 out of 0 atoms, i = 0 out of 1 capacity.
> Segmentation fault (core dumped)
I didn't write the xtalsymm command, but the "0 out of 0 atoms"
messages seems like a problem. Maybe the atom mask you are using isn't
selecting what you think it is? You could test it separately with
something like the 'atoms' command to check,. Beyond that I would need
you to send me off-list the topology and 2 or 3 frames of the
trajectory so I can try to reproduce the segfault.
>
> By using "parmbox x 64.7 y 64.7 z 65.2 alpha 90 beta 90 gamma 120" I
> could disable the warnings, but the seg fault remained.
Unless the trajectory doesn't contain any unit cell info or you have a
really good reason, it's generally not a good idea to overwrite the
box info in a trajectory (which is usually more up to date than what
is in the topology).
-Dan
>
> Thanks in advance,
> Thorben
>
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Received on Tue Jan 17 2023 - 05:30:03 PST
