From: John Stone (
Date: Sat Dec 03 2016 - 22:48:02 CST

  The .nc file is an AMBER trajectory stored in a NetCDF file.
I'm not sure about the .topo topology file, that's not familiar to me,
perhaps that's what they used to call a "PARM" file?

The Unix/Linux and Mac versions of VMD contain a NetCDF plugin that
can read the AMBER .nc files.

Unix compilation of the NetCDF plugins has historically been straightforward,
particularly the older NetCDF 3.x library, which is all that's needed for
the existing AMBER formats supported by the NetCDF plugin.
In principle, the VMD NetCDF plugin itself should compile fine on Windows,
however this requires matching the version of the MS compilers used for VMD
and NetCDF against each other, and thus far we haven't had a VMD build
that matched what the pre-built NetCDF libs were built with.

I have looked at compiling the NetCDF-C libraries for Windows, but the
procedures for building them are complex since they now have dependencies
on HDF5 as well, and again, the last time I went for it,

I discovered that we were using compilers that were (at that time)
too new for NetCDF/HDF. Looking at the latest NetCDF library it appears
they are now using MSVS 2012, which is a big step forward since I
last looked. The issues with dependencies on HDF5 etc still remain,
but it's the compiler versions that are more critical due to
sensitivities there with other libraries and runtimes we link against for
core parts of VMD. Here's the NetCDF page of interest that describes
their existing binary release and source compilation methodology:


On Sat, Dec 03, 2016 at 09:33:16PM -0500, James Kress wrote:
> I have two files from an AMBER simulation, and vacuo.topo
> How do I use VMD to visualize these files? is a binary file
> containing the trajectory information. vacuo.topo is the associated AMBER
> topology file.
> Thanks.
> Jim Kress

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349