AMBER Archive (2008)

Subject: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory

From: Ian (
Date: Fri Jun 06 2008 - 04:19:58 CDT

Hello All,

I am having difficulties using ptraj (v9.0) to strip a trajectory so that
the only atoms remaining are those within a given distance of a particular
residue. According to the ambmask section of the AMBER 9 manual, this should
be possible using something like:

strip [:45 <@5.0]

However, ptraj just seems to freeze when executing this command, both for a
large protein trajectory and a completely unrelated trajectory of a small (8
residue) peptide. By "freeze", I mean there is no activity (output/messages)
for at least 10 minutes. Without parentheses [], the above example just
strips out the atoms of residue 45. Likewise if I replace the parentheses
with double quotes (this should apparently force the use of a newer parser).

I have used the "checkmask" command in rdparm as a second check on all this,
and get the same behavior.

Is it possible to perform this kind of operation with ptraj? If so, what I
am doing wrong here?

Any help would be greatly appreciated,


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