Michael,
None of the official releases have Amber trajectory support (although
the mac 0.84 beta may have an early version of this code). I'm planning on
another release near the end of September.
If you can build from the CVS repository, then you can use the code today:
(1) make sure that your trajectory and topology files have the same prefix and
end in .top and .trj respectively. Also make sure that your topology exactly
corresponds to the trajectory file (you may need to create a new topology file
if you've deleted some atoms from the trajectory).
(2) Now load them:
load parm.top
load_traj parm.trj
help load_traj
has some additional options, such as start, stop, average, interval,
selection...
So long as trajectories are generated from the same topology, you can
concatentate them as follows:
load_traj part1.trj,parm
load_tram part2.trj,parm
load_traj part3.trj,parm
For now, you'll probably want to preprocess your trajectory using ptraj in
order to center, average, and perhaps to remove waters. And you'll need to
create a new topology file reflecting any atom deletions. Tom Cheatham and I
are talking about trying to fold a copy of ptraj into PyMOL, but don't have any
definite plans yet.
Cheers,
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 FAX:(650)-266-3501
