AMBER Archive (2009)

Subject: AMBER: problem with ptraj image command in Amber 10?

From: Ryan Pavlovicz (
Date: Tue Jan 06 2009 - 11:28:27 CST

I seem to be getting different (bad) results when processing a trajectory
with the image command of ptraj from the Amber10 release than when the same
trajectory is processed with the same commands from the Amber9 release.

I was trying to image waters from a PBC MD run -- but when this was done
with the Amber10 ptraj, there was some overlap of the waters with the
protein. The imaging from Amber9 looked reasonable.

Has anyone else run into this problem?


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