RE: [PyMOL] Re: Amber

[DeLano, W. <wa...@su...>]

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:wa...@su...
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