[AMBER] pytraj

From: Pietro ARONICA <pietroa.bii.a-star.edu.sg>
Date: Wed, 18 Nov 2020 17:03:45 +0000

Hello all,
Has there been an update to pytraj in the past 24-48 hours? My code, which relies on the python implementation of cpptraj, no longer works. It reads trajectory and restart files fine, as far as I can tell; they seem to have all the correct box parameters. However, using pytraj.write_traj to write them into pdb gives a file where the CRYST1 record either has all zeroes for the box, or the first one is a zero and the others are correct. Furthermore, it also outputs the coordinates of all waters as nan. This code worked perfectly fine up to a few days ago, so I'm wondering what happened. Trying different pytraj commands like load, save and write_traj with different options do not seem to solve the issue; in each case, the CRYST1 records are incorrect and in some cases the waters have nan coordinates.
The problem seems to be only with pytraj. Loading, reading and writing the same files with the interactive, normal version of cpptraj has no issue, but my workflow requires the python implementation.
Does anyone have any clues?
This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.
AMBER mailing list
Received on Wed Nov 18 2020 - 09:30:02 PST
Custom Search