Re: [AMBER] problem loading the trajectory files in vmd

From: Matias Machado <>
Date: Mon, 06 Dec 2021 18:55:07 -0300 (UYT)

Dear Ankita,

VMD 1.9.3 is able to read all AMBER file formats in Linux and Windows, but there is an issue reading ".ncrst" in Mac.

Most likely the automatic detection of the file extension failed due to a wrong naming...

The extension ".mdcrd" is quite old and well supported in VMD. But you should check that you "mdcrd" is actually in the old ACII file format (I suspect this is the problem). if it is binary (the default output in new AMBER versions) then it is a NetCDF file. Hence the correct extension that is automatically detected by VMD is ".nc" (for trajectories) or ".ncrst" (for a restart file).

To manually load a NetCDF file select "NetCDF (AMBER, MMTK)" in the "Molecule file browser" window of VMD...

Hope it helps,


Protein Engineering Unit
Institut Pasteur de Montevideo
Mataojo 2020, Montevideo, 11400, Uruguay

----- Mensaje original -----
De: "Priya Dey" <>
Para: "AMBER Mailing List" <>
Enviados: Viernes, 3 de Diciembre 2021 8:58:20
Asunto: Re: [AMBER] problem loading the trajectory files in vmd

The .mdcrd file format is not readable in VMD software.
First, you have to convert '.mdcrd' file into a readable format, for
example '.pdb' with the help of cpptraj. Then, the .pdb file can be opened
using VMD software.

On Fri, Dec 3, 2021 at 4:22 PM ankita mehta <> wrote:

> Hello,
> I am trying to load the trajectory files .mdcrd files in vmd on windows.
> My simulations were run on Amber.
> But everytime i load the files , the following error message is displayed
> on the vmd windows.
> It says " problem reading the crd file".
> I followed following steps:
> 1. select "new molecule "
> 2. Load "parm file " and select file type as "Amber parm 7".
> 3. Then load the trajectory file as "mdcrd" file and select file type as "
> Amber coordinates' '.
> 4. error message displays on the VMD windows "Problem reading CRD file".
> P.S. - -I have a windows operating system.
> Any help is appreciated !
> TIA!
> Ankita
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Received on Mon Dec 06 2021 - 14:00:02 PST
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