On Fri, Aug 8, 2014 at 10:35 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> OK, I think the issue is that you are trying to load your stripped
> cluster trajectory (i.e. trajectory without water) with your original
> topology. What you want to do is add something like 'outprefix nowat'
> to your 'strip' command. This will write out a stripped topology named
> nowat.<original topology name> that will correspond to your cluster
> trajectories/representatives. Also, unless you're using vmd on windows
> I really recommend using the netcdf format, 'clusterfmt netcdf', as
> this format is superior to the Amber ASCII trajectory format in every
> way.
>
Will using the .nc filename extension not use NetCDF by default? That's
what the OP did...
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Aug 08 2014 - 08:00:03 PDT
