From: Francesco Pietra (
Date: Sun Mar 14 2010 - 04:51:02 CDT

I have carried out many runs for the exit of the ligand from the
protein. I can confirm that, with the commands described previously
(please see below previous mail), the trace does not start from where
the ligand starts leaving. It starts later on and not exactly on the
actual path, as monitored from VMD Main, once, step 5, speed slow. In
the most complex path for ligand exit, the trace (red on "scale")
starts on the rear of a helix with respect to the initial position of
the ligand. I.e., the initial position of the ligand can't be seen
from where the trajectory_path trace begins. Also, the trace continues
on the right side of the helix, while the actual ligand path develops
on the the left of the helix. The trajectory path describes
more-or-less correctly how the ligand spends a lot of time trapped in
a potential well, and the direction of exit is correctly indicated by
the blue trace, but there is a shift with respect to the actual path.
In this case a serious discrepancy with respect to proximity to the
helix residues. All that neatly detected with either ribbon or cartoon
representations of the protein

I wonder where I am incorrectly performing. I don't see a log file to
send for inspection.

Thanks for help

francesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <>
Date: Sun, Mar 7, 2010 at 9:55 AM
Subject: trajectory_path.tcl queries
To: vmd <>

New to trajectory_path.tcl, I dare placing a question. In my usage

source trajectory_path.tcl
set myligand [atomselect top "resid for.myligand"]
trajectory_path $myligand scale (which, grossly scales from red to
yellow, cyan and finally blue)

there is a large shift in the coordinate scale between the path that
can be followed from VMD Main and that described with
trajectory_path.tcl.  Also, although the two are identical, the latter
is on a much smaller scale. The shift is so large that the path
described with trajectory_path.tcl is seen entirely at the immediate
outside of the protein.

francesco pietra