Re: [AMBER] volume in pytraj?

From: Hai Nguyen <>
Date: Mon, 19 Aug 2019 12:06:45 -0400

On Mon, Aug 19, 2019 at 9:51 AM Shayna Hilburg <>

> pytraj.Trajectory is the one I had been using (because it was necessary for
> me to get the mean structure in a prior calculation) that does not work for
> pytraj.volume.

Does it (the one from using pytraj.Trajectory directly) has unitcells of
None or 2d array? does its topology have a legit box (example below)?

For example:
In [32]: traj.unitcells.shape

Out[32]: (10, 6)

In [33]:

Out[33]: <Box: ortho, (x, y, z, alpha, beta, gamma) = (39.455974,
46.821517, 40.469541, 90.0, 90.0, 90.0)>

If none of the above are available, I think your workflow needs to update

PS: Above is just FYI since you're already solved your case.

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Received on Mon Aug 19 2019 - 09:30:02 PDT
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