Hi,
As others have noted, the space group warnings are innocuous and can
be safely ignored.
The real error is here:
> Operation not supported
> Error: Opening Netcdf file cluster.c0 for Write.
This seems like a filesystem error. Is there enough space on the
device? Are you writing to a directory you have permission for? It
would help to at least see the full cpptraj input you are using and to
know what version you are running.
-Dan
On Tue, Jul 19, 2022 at 8:53 AM Saranya vasudevan via AMBER
<amber.ambermd.org> wrote:
>
> While analyzing the trajectories in cpptraj for cluster, I got the
> following errors:
>
> Writing 'cluster.c0' as Amber NetCDF
> Operation not supported
> Error: Opening Netcdf file cluster.c0 for Write.
> Error: Could not set up cluster trajectory cluster.c0 for write.
> Writing 'clusteroutname.c0.pdb' as PDB
> Warning: No PDB space group specified.
> Warning: Set 1; unit cell is not X-aligned. Box cannot be properly
> stored in PDB CRYST1.
> Writing 'clusteroutname.c1.pdb' as PDB
> Warning: No PDB space group specified.
> Warning: Set 1; unit cell is not X-aligned. Box cannot be properly
> stored in PDB CRYST1.
> Writing 'clusteroutname.c2.pdb' as PDB
> Warning: No PDB space group specified.
> Warning: Set 1; unit cell is not X-aligned. Box cannot be properly
> stored in PDB CRYST1.
> Writing 'clusteroutname.c3.pdb' as PDB
> Warning: No PDB space group specified.
> Warning: Set 1; unit cell is not X-aligned. Box cannot be properly
> stored in PDB CRYST1.
> Writing 'clusteroutname.c4.pdb' as PDB
> Warning: No PDB space group specified.
> Warning: Set 1; unit cell is not X-aligned. Box cannot be properly
> stored in PDB CRYST1.
> Cluster timing data:
>
>
> Is there a way to troubleshoot this?
>
>
>
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Received on Thu Aug 04 2022 - 13:35:08 PDT
