Hi,
On Thu, Mar 10, 2022 at 2:46 AM <chanyann06.stu.scu.edu.cn> wrote:
>
> 0% 10% 20% 30% Warning: Frame 14529 imaging failed, box lengths are zero.
>
> Warning: Frame 14530 coords 1 & 2 overlap at origin; may be corrupt.
>
> Warning: Frame 14530 imaging failed, box lengths are zero.
As the messages indicate, certain frames in your trajectory file are
corrupted (with NetCDF files this usually manifests as all coordinates
being 0, which cpptraj is catching here). Those frames are not usable
and should be discarded.
>
> terminate called after throwing an instance of 'std::bad_alloc'
I think this was a bug in the 'check' command that I fixed. What
version of cpptraj are you using. If not the GitHub version, can you
try using that and see if the behavior is fixed? Thanks,
-Dan
>
> what(): std::bad_alloc
>
>
>
> It is confusing that the frames before and after the warning frames (14530-25099 frames report warnings) seem normal. Can the frame 14529 ( the one before warning) and frame 25100 (the one after warning) be continuous? What would cause this warning?
>
> I've check similar problems in amber mailing list but could not sovle it.
>
> Looking forward to your help and thanks a lot!
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 10 2022 - 10:00:02 PST
