Hi,
On Sun, Nov 10, 2024 at 11:45 PM Guberman-Pfeffer, Matthew via AMBER
<amber.ambermd.org> wrote:
>
> Warning: Set 1; unit cell is not X-aligned. Box cannot be properly stored as Amber NetCDF trajectory.
When you RMS-fit in cpptraj, the atom coordinates and unit cell
vectors are rotated according to the calculated best-fit rotation. In
the Amber NetCDF format (along with many other trajectory formats),
unit cell vectors are stored as 3x lengths and 3x angles - 6 numbers
total. The reason this works is that the unit cell is assumed to be
X-aligned; i.e. the unit cell X vector is colinear with the global X
axis vector (the Y and Z components of the X-axis vector coordinate
are 0). Once you rotate the unit cell vectors the unit cell X-axis
vector is no longer colinear, so the unit cell can no longer be
described with just 3x lengths and 3x angles. The consequence of this
is that imaging will no-longer work properly with that trajectory,
which is why cpptraj prints the warning. If you want to keep the
rotated unit cell vectors, the only solution at the moment is to use a
trajectory format that stores the full unit cell vector coordinates
(like TRR or XTC). If you don't care about the unit cell
vectors/imaging, you can just remove the unit cell information with
the 'nobox' keyword of 'trajout'.
Hopefully this makes sense.
-Dan
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Received on Mon Nov 11 2024 - 06:30:01 PST
