Re: [AMBER] Tutorial B1 problems

From: David A Case <>
Date: Wed, 4 Jul 2018 21:19:38 -0400

On Mon, Jul 02, 2018, Jennifer L. Muzyka wrote:

> We are working through Tutorial B1: Simulating a small fragment of DNA
> and are struggling with section 3
> The sander output files look fine in xmgrace. But when we open the
> files in VMD, we get the error message shown below.
> Info) Using plugin crd for coordinates from file
> /Users/daniel.thompson/Desktop/AMBERtest/polyAT_vac_md1_12Acut.mdcrd
> Problem reading CRD file

The default trajectory file format has changed, it is now NetCDF.

If you are using VMD on Windows, you cannot read these files. You will need
to re-run the simulation, setting ntxo=1 (I think: please check the manual)

If you are using Linux or Mac, be sure to set the input file format to
"netcdf" in VMD.


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Received on Wed Jul 04 2018 - 18:30:02 PDT
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