Apologies in advance for the probable silliness of this question, but
with the 14 Apr release candidate of AmberTools (compiled with
"-nobintraj -noX11 -nosleap gnu"), the following ptraj commands do not
generate an average structure in foo.pdb, whereas they do with the
AMBER 10-era ptraj:
trajin md5.trj.gz
average foo.pdb
go
...where md5.trj.gz is a gzipped mdcrd trajectory. It isn't clear to
me from the documentation in CVS (or else I missed it) how my commands
are incorrect. I have the same (lack of) result with CVS AMBER 11's
AmberTools. The ptraj output is below.
Thanks,
--Tom
$ $AMBERHOME/bin/ptraj solute.pdb
\-/
-/- PTRAJ: a utility for processing trajectory files
/-\
\-/ Version: "AMBER 11.0 integrated" (4/2010)
-/- Executable is: "/home/josept02/build/14apr10/amber11/bin/ptraj"
/-\ Running on 1 processor(s)
\-/ Reading PDB file "solute.pdb": 12004 atoms found!!!
Found 720 residues
PTRAJ: Processing input from "STDIN" ...
trajin md5.trj.gz
PTRAJ: trajin md5.trj.gz
Checking coordinates: md5.trj.gz
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: md5.trj.gz
If this is not a compressed file then there is a problem
Rank: 0 Atoms: 12004 FrameSize: 291723 TitleSize: 81 NumBox: 3 Seekable 0
average foo.pdb pdb
PTRAJ: average foo.pdb pdb
Mask [*] represents 12004 atoms
go
[No output trajectory specified (trajout)]
PTRAJ: Successfully read the input file.
Coordinate processing will occur until EOF (unknown number of frames).
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (md5.trj.gz) is an AMBER trajectory (with box info)
NO OUTPUT COORDINATE FILE WAS SPECIFIED
ACTIONS
1> AVERAGE: dumping the average of the coordinates to file foo.pdb
start: 1 Stop [at final frame] Offset: 1
Atom selection * (All atoms are selected)
Output file information: File (foo.pdb) is a PDB file
Processing AMBER trajectory file md5.trj.gz
Set 1 .................................................
- snip -
Set 3950 .................................................
Set 4000 100%
PTRAJ: Successfully read in 4000 sets and processed 4000 sets.
Dumping accumulated results (if any)
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Received on Fri Apr 16 2010 - 13:00:02 PDT
