AMBER Archive (2008)

Subject: AMBER: ptraj has trouble with x-plor psf file from VMD

From: Dong Xu (
Date: Thu May 29 2008 - 15:23:56 CDT

Hi All,

I'm having problem with ptraj processing x-plor psf file generated
from VMD. The ouput looks like:

  -/- PTRAJ: a utility for processing trajectory files
  \-/ Version: "Cheatham lab development full version 9.9h" (4 April 2008)
  -/- Executable is: "ptraj"
  \-/ Reading in CHARMM PSF file
Reading in the title...

 REMARKS VMD generated structure x-plor psf file

Total number is atoms is 7614
Reading in the atom information...
Dumping out residue names:
 N N C1 C1 C2
Dumping state information...
  atoms: 7614
  residues: 5
  box length: 0.000 0.000 0.000
  box angles: 90.000 90.000 90.000
  molecules: 487
  max frames: 0

PTRAJ: rms first out rms_fit21stpsf.txt :110-262_at_CA,C,N,O
Mask [:110-262_at_CA,C,N,O] represents 0 atoms !!!NO ATOMS DETECTED!!!
[No output trajectory specified (trajout)]

Obviously the residue names are read incorrectly and mask selection is
not accepted either. Is this caused by the difference between x-plor
psf file and CHARMM psf file?
Reading DCD trajectory file works fine and pdb/dcd combination also works.


Dong Xu
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