Hi Elvis,
Thanks for your email. My question was different.
I want to save the .nc files during MD in such a way that I don't need to
use cpptraj later to reimage/center etc.
The .rst files are written during MD and they don't need to be reimaged in
my experience, so can't the .nc
be written that way during MD?
Ravi
On Tue, Sep 26, 2017 at 12:37 AM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> 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 - 07:00:02 PDT
