On Mon, Apr 11, 2011 at 10:03 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
> Dear Jason,
>
> I am sorry. By mistake the lower portions of file got deleted.
> The problem is I am getting only 10 output pdb s from this script
> where I should get 41 structures named 2b5e.new.pdb.1/.... 2b5e.new.pdb.41.
>
Ah. It could be that ptraj appends the trajectory frame number to the end
of the file, not the total frame number that it has accumulated over all of
the frames read in. Basically, each trajectory creates the files
2b5e.new.pdb.1 through 2b5e.new.pdb.10, and resets every time a new
trajectory is reached.
Thus, the 10 frames you see are just from the last trajectory you read in.
If this is true (a ptraj expert would have to confirm), then the way to do
what you want to do is run it in 2 steps. First, combine all of the
trajectories/snapshots into a single trajectory, then in a separate step,
extract the PDBs.
> I am sorry I did not understand well what you mean by "it'll have
> numbers appended to it".
>
It means the file names will not be 2b5e.new.pdb, it will be 2b5e.new.pdb.1,
2b5e.new.pdb.2, ... etc.
Hope this helps,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 11 2011 - 10:30:04 PDT
