Re: [AMBER] Visualizing the system trajectory from .nc file

From: Emmett Leddin <>
Date: Fri, 11 Sep 2020 00:29:18 -0500

Hello Jatin,

This part of the tutorial refers to visualizing the structures using a different program. Most people accomplish that by using VMD (

The nc extension is used for the NetCDF file format. VMD has a NetCDF plugin, and if that has been installed you can do “vmd -parm7 file.prmtop -netcdf” to open it (or specify it using the File Load GUI). If I remember correctly, the NetCDF plugin isn’t supported on Windows machines.

The final frame (so what should be at 300 K) is saved in the .rst file. You can also load just that file using “vmd -parm7 file.prmtop -rst7 file.rst”. Hope that helps!


Emmett Leddin

Pronouns: he/him
Chemistry PhD Candidate

>> On Sep 10, 2020, at 23:36, Jatin Kashyap <> wrote:
> Dear AMBER Community,
> I am following the protein-ligand tutorial.[1] I was able to reproduce it until the last step. But I am not able to visualize the binary trajectory file generated in the very last step (.nc).
> As this is the first time I came across this file format. Can anybody please guide how to follow the last part of the instructions.[2]
> Thank you very much.
> [1]
> [2]
> “you can take a look at the snapshot at 300K"
> ——
> Jatin Kashyap
> Ph.D. Student
> Dr. Dibakar Datta Group
> Department of Mechanical and Industrial Engineering
> New Jersey Institute of Technology (NJIT)
> University Heights
> Newark, NJ 07102-1982
> Phone- (201)889-5783
> Email-
> _______________________________________________
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Received on Thu Sep 10 2020 - 22:30:02 PDT
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