Re: [AMBER-Developers] final (!?!) release candidate for Amber11

From: Tom Joseph <>
Date: Fri, 16 Apr 2010 15:53:45 -0400

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

...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.


$ $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
[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:

  File (md5.trj.gz) is an AMBER trajectory (with box info)

  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)

AMBER-Developers mailing list
Received on Fri Apr 16 2010 - 13:00:02 PDT
Custom Search