HI,
BY default AMBER16 will save trajectories and restart files in netcdf format . However, you must not zip the netcdf trajectories, as cpptraj cannot read those zipped netcdf trajectories.
IF you have saved amber trajectories, you can load the trajectories in cpptraj and save them as netcdf trajectories.
Use this command
parm <name>.prmtop
trajin <name>.[mdcrd/crd]
autoimage
trajout <name>.nc netcdf
run
Hope this helps
Best Regards
Elvis Martis
Mumbai, INDIA.
________________________________________
From: Ravi Abrol <raviabrol.gmail.com>
Sent: 26 September 2017 11:21
To: AMBER Mailing List
Subject: [AMBER] How to save reimaged trajectory file during MD?
Hello All,
We have had a hard time with some reimaging of protein-protein complexes in
a membrane
after MD, even though we use iwrap=1.
The .rst files are always proper.
Is it possible to write the .nc files during MD in the same way the .rst
files are written out? I couldn't find this option. If this option doesn't
exist, is it possible to add it in a future release?
Thanks,
Ravi
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Received on Tue Sep 26 2017 - 01:00:04 PDT
