AMBER Archive (2007)

Subject: AMBER: ptraj bug? -- doesn't like restart files from REMD

From: Nicolas Lux Fawzi (fawzin_at_berkeley.edu)
Date: Thu Feb 22 2007 - 15:33:58 CST

I think ptraj doesn't like restart files from replica exchange, due to
the additional field in the first of second line with the time information?
I'm trying to turn a restart file into a pdb file using ptraj:

Here's the contents of my ptrajscript:
$ cat ptraj_script
trajin restrt.rep2
strip :WAT
trajout file.pdb pdb

Here's the head of my restrt.rep2 file:
$ head restrt.rep2
                                                                                

 4862 0.4784300E+05 0.3510000E+03
  16.7917954 26.8320973 19.7609974 15.8343008 26.4962545 19.5918673
  17.0375465 27.7002989 19.3248016 16.7891954 26.9821245 20.7508589
  17.7929679 25.7884446 19.5200394 18.7741891 26.2232656 19.8800869
  17.4068614 24.5561744 20.3664887 18.1907567 23.8562099 20.2266631
  17.3015416 24.7801046 21.4745089 16.5596423 24.0943526 19.8892102
  17.9106884 25.5049114 18.0221486 17.4944962 24.4350937 17.5945007
  18.3688125 26.5178413 17.2130347 18.7206088 27.3543308 17.7384760
  18.4257704 26.5020327 15.7325866 18.4236115 25.5333617 15.1832622

If I remove the " 0.3510000E+03" from the second line, it works fine.
If I leave it in, here's what I get (and since the single frame is
"corrupted", I get no pdb files). I've figured out how to do this
manually, but it seems like it would be nice to have this work in the
future:

$ptraj ../peptide.top < ptraj_script

  \-/
  -/- PTRAJ: a utility for processing trajectory files
  /-\
  \-/ Version: "AMBER 9.0 integrated" (April 2006)
  -/- Executable is: "ptraj"
  /-\
  \-/ Residue labels:

 blah blah

PTRAJ: Processing input from "STDIN" ...

PTRAJ: trajin restrt.rep2
  Checking coordinates: restrt.rep2

PTRAJ: strip :WAT
Mask [:WAT] represents 4734 atoms

PTRAJ: trajout file.pdb pdb

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 3 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (restrt.rep2) is an AMBER trajectory (with box info) with 3 sets

OUTPUT COORDINATE FILE
  File (file.pdb) is a PDB file

ACTIONS
  1> STRIP: 4734 atoms will be removed from trajectory: :12-1589

Processing AMBER trajectory file restrt.rep2

WARNING in readAmberTrajectory(): Set #1 is corrupted ( 4862
0.4784300E+05 0.)...

PTRAJ: Successfully read in 0 sets and processed 0 sets.
       Dumping accumulated results (if any)

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