Re: [AMBER] Cluster results

From: Jason Swails <>
Date: Fri, 8 Aug 2014 10:40:15 -0400

On Fri, Aug 8, 2014 at 10:35 AM, Daniel Roe <> 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
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Aug 08 2014 - 08:00:03 PDT
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