" 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."
Unless you are running VMD under Windows. It is my understanding, and
experience, netCDF trajectory files are not supported, at least not throough
v1.9.3
Jim
-----Original Message-----
From: David A Case <david.case.rutgers.edu>
Sent: Sunday, May 13, 2018 2:00 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Novice Question: MD Visualisation in VMD
On Sun, May 13, 2018, Billy Williams-Noonan wrote:
>
> When I load my system.top 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.
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Received on Sun May 13 2018 - 12:30:02 PDT
