Re: [AMBER] Novice Question: MD Visualisation in VMD

From: David A Case <>
Date: Sun, 13 May 2018 13:59:33 -0400

On Sun, May 13, 2018, Billy Williams-Noonan wrote:
> When I load my file into VMD for the coordinates and add the
> trajectory data (em.mdcrd or nvt.mdcrd), no frames load into the coordinate
> file. Do I need a .prmtop file instead? I have been following the
> instructions on the tutorial linked earlier.

Let me add a little to Anselm's excellent post:

Amber doesn't enforce file or extension names. This allows users to
call things what they want, but can make communication difficult.

Both Amber and GROMACS have "topology" files. Amber users might often
use .top, .prmtop, or .parm7 as an extension for these files. If you
use .parm7, VMD will automatically recognize the extension and do the
right thing. And, and Anselm pointed out, you do need to load an Amber
prmtop file into VMD before loading a trajectory file.

Trajectory filenames are also up to the user. Historically, the .mdcrd
extension was used, but the actual file name depends on the commands you
give to sander. To make things (somewhat) more confusing; Amber has
both formatted and binary (netCDF) formats for trajectory files.
Starting with Amber 16, the default format is netCDF, although the user
can request a formatted form via the ntxo variable.

It is, therefore, entirely possible that sander could create a foo.mdcrd
file that is actually a netCDF file. If a trajectory file is formatted,
you need to tell that to VMD by choosing either "Amber coordinates" or
"Amber coordiantes with box"; if the file is netCDF, choose the "netCDF"
option (here is doesn't matter if the simulation is periodic or not).

...hope this helps....dac

p.s., FWIW: I personally use a .parm7 extension for Amber prmtop files,
and a .nc extension for netCDF trajectory files. I always choose the
(default) netCDF format for both trajectory and restart file.

AMBER mailing list
Received on Sun May 13 2018 - 11:30:03 PDT
Custom Search