Re: [AMBER] .rst and .mdcrd file outputted in ascii

From: David A Case <>
Date: Wed, 2 May 2018 14:36:59 -0400

On Wed, May 02, 2018, Daniela Kohen wrote:
> I am adapting the “Simulating a DNA polyA-polyT Decamer” tutorial for
> my class (as I have for years) and all goes great until I need to use a
> .mdcrd file that is created when I run sander. The file is in ascii, I
> think, and I can not upload it in VMD.

Are you sure the file is ascii? (Type "file foo.mdcrd" to see). The
new default (starting with Amber16,) is that trajectory files are now
binary (netcdf) files. If so, change the name to, and VMD will
automatically recognize the format from the .nc extension; or choose
netcdf as the format when you load that file, whatever its extension.

> VMD determines its file type to be AMBER coordinates but can not read it.

Not sure if the above is actually your problem, but it's worth a try.

...good luck....dac

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Received on Wed May 02 2018 - 12:00:02 PDT
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