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.CA,C,N,O
Mask [:110-262.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.
Thanks,
Dong Xu
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Received on Sun Jun 01 2008 - 06:07:39 PDT
