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,
Ian.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Jun 08 2008 - 06:07:50 PDT
