Re: [AMBER] Troubles with making a movie in VMD,

From: Daniel Roe <>
Date: Tue, 9 Jul 2013 13:43:05 -0600


On Tue, Jul 9, 2013 at 1:34 PM, Hunter Brown <> wrote:
> Oh! Sorry, 2500 is just an arbitrarily large number given to ptraj. The actual number of frames in each trajectory is 1250.

FYI in cpptraj you can use 'last' instead of some arbitrarily large
number to indicate you want to use the last frame, e.g.

trajin mdcrd 1 last 5

> I was able to get the 1,000 frames in VMD by loading a pdb file of my system, and then loading the mdcrd file for that pdb. Before I had tried loading the prmtop as the molecule (which only gave me 189 frames for some reason).

This indicates that the topology you were using did not correspond to
your trajectory. Did the coordinates appear "jumbled" when you loaded
using the topolgy file? This is an issue when e.g. you load a stripped
trajectory with the original solvated topology file. If possible I
recommend using netcdf trajectories in the future since there is
better error checking compared to ASCII trajectories (in addition to
them being more efficient overall).

> Actually, it is odd to me that loading the prmtop as a molecule, and then the trajectory for it did anything at all, because prmtops do not contain any coordinates, no?

Loading the prmtop separate from coordinates makes a lot of sense.
Loading the prmtop file just tells VMD/cpptraj/ptraj or any other
program about the overall topology of the molecule. In other words, it
tells the program how to expect any coordinates you might load to be
organized. This allows much more flexibility.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Jul 09 2013 - 13:00:04 PDT
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