Thank you. It worked! We ended up using the .crd file as an extension and
Amber Coordinates with periodic box as the option on VMD.
-Suchetana
On Mon, Mar 14, 2022 at 11:45 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> trajin the netcdf, and then give a command trajout. More details are in the
> cpptraj manual. The flags will let you reduce the number of frames by
> skipping some, and set the format (you probably want "Amber trajectory",
> which you can also get by default if you use .crd at the end of the file
> name).
> https://amberhub.chpc.utah.edu/trajout/
>
>
> On Mon, Mar 14, 2022 at 2:26 PM Suchetana Gupta <tutulg.gmail.com> wrote:
>
> > Hi
> > Thanks for the response. While a virtual box is one option, it is
> probably
> > a bit tedious. I would be more interested to know about the second
> option.
> > Trajin with a .nc file. What do you mean by the ascii version for
> trajout?
> > I tried reading the .cdf files using Amber7 Coordinates with Periodic box
> > option, yet it returned error.
> > Can you please help me with more details?
> > Thanks
> > Suchetana
> >
> >
> > On Mon, Mar 14, 2022 at 4:43 AM Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > You can use cpptraj on Linux to convert them to ascii versions using
> > > trajin/trajout, and read those in windows.
> > >
> > > On Mon, Mar 14, 2022, 1:09 AM Suchetana Gupta <tutulg.gmail.com>
> wrote:
> > >
> > > > Hi
> > > > I have been using VMD on a linux machine all along. However, now I do
> > not
> > > > have access to one for some reason. Now that I have installed VMD on
> > > > Windows, I find that this version does not have an option to read .nc
> > > files
> > > > (netcdf).
> > > > What is a possible solution?
> > > > Thanks
> > > > Suchetana Gupta
> > > > University of Oregon
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Received on Mon Mar 14 2022 - 13:00:03 PDT
