Hello All,
I wish to calculate the diffusion coefficients of crystal structure ions for
my nucleic acid system, for which I need to remove the "imaging" problem in
trajectories. I have generated CHARMM dcd files with CHARMM psf topology
files. The numbering of the nucleic acids starts from 2 to 173 and the ions
numbering of question are 821, 200-231.
I am using the script as:
trajin abg-tot-25ns.dcd
center :2-173 mass origin
image origin center byres ":821,200-231" familiar com :2-173
trajout abgimg.pdb pdb nobox
What I am getting the output of running this script is as: ptraj
abg-ionized-mod.psf image.in
\-/
-/- PTRAJ: a utility for processing trajectory files
/-\
\-/ Version: "AMBER 10.0 integrated" (2/15/2008)
-/- Executable is: "ptraj"
/-\
\-/ Reading in CHARMM PSF file
Reading in the title...
REMARKS original generated structure x-plor psf file
REMARKS 2 patches were applied to the molecule.
REMARKS topology
/usr/local/lib/vmd/plugins/noarch/tcl/autoionize1.2/ions.top
REMARKS topology 3dil-nolys_autopsf-temp.top
REMARKS topology /usr/local/lib/vmd/plugins/noarch/tcl/solvate1.2/wat.top
REMARKS segment N1 { first 5TER; last 3TER; auto angles dihedrals }
REMARKS segment O1 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O2 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O3 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O4 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O5 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O6 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O7 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O8 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O9 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment O10 { first NONE; last NONE; auto angles dihedrals }
REMARKS segment WT1 { first NONE; last NONE; auto none }
REMARKS segment WT2 { first NONE; last NONE; auto none }
REMARKS segment WT3 { first NONE; last NONE; auto none }
REMARKS segment WT4 { first NONE; last NONE; auto none }
REMARKS segment WT5 { first NONE; last NONE; auto none }
REMARKS segment WT6 { first NONE; last NONE; auto none }
REMARKS segment WT7 { first NONE; last NONE; auto none }
REMARKS segment WT8 { first NONE; last NONE; auto none }
REMARKS segment IO2 { first NONE; last NONE; auto none }
REMARKS patch 5TER N1:2
REMARKS patch 3TER N1:173
Total number is atoms is 53232
Reading in the atom information...
Dumping out residue names:
GUA GUA CYT CYT GUA ADE CYT GUA GUA ADE
GUA GUA CYT GUA CYT GUA CYT CYT CYT GUA
ADE GUA ADE URA GUA ADE GUA URA ADE GUA
GUA CYT URA GUA URA CYT CYT CYT ADE URA
CYT ADE GUA GUA GUA GUA ADE GUA GUA ADE
ADE URA CYT GUA GUA GUA GUA ADE CYT GUA
GUA CYT URA GUA ADE ADE ADE GUA GUA CYT
GUA ADE GUA GUA GUA CYT GUA CYT CYT GUA
ADE ADE GUA GUA GUA URA GUA CYT ADE GUA
ADE GUA URA URA CYT CYT URA CYT CYT CYT
GUA CYT URA CYT URA GUA CYT ADE URA GUA
CYT CYT URA GUA GUA GUA GUA GUA URA ADE
URA GUA GUA GUA GUA ADE ADE URA ADE CYT
CYT CYT ADE URA ADE CYT CYT ADE CYT URA
GUA URA CYT ADE CYT GUA GUA ADE GUA GUA
URA CYT URA CYT URA CYT CYT GUA URA GUA
GUA ADE GUA ADE GUA CYT CYT GUA URA CYT
GUA GUA URA POT SOD SOD SOD SOD SOD SOD
SOD SOD SOD SOD SOD SOD SOD SOD SOD SOD
...
SOD SOD SOD MG POT POT TIP3 TIP3 TIP3 TIP3
TIP3 TIP3 TIP3 TIP3 TIP3 TIP3 TIP3 TIP3 TIP3 TIP3
...
TIP3 TIP3 TIP3 TIP3 TIP3 TIP3 TIP3 SOD SOD SOD
SOD SOD SOD SOD SOD SOD SOD SOD SOD SOD
...
SOD SOD SOD SOD
Dumping state information...
atoms: 53232
residues: 16174
box length: 0.000 0.000 0.000
box angles: 90.000 90.000 90.000
molecules: 20
max frames: 0
solvent molecules: 15831 (47493 atoms)
solvent mask is: :1,:207-16037
PTRAJ: Processing input from file image.in
PTRAJ: trajin 3dil-nolys-tot-25ns-dt10.dcd
Checking coordinates: 3dil-nolys-tot-25ns-dt10.dcd
PTRAJ: center :2-173 mass origin
Mask [:2-173] represents 5569 atoms
PTRAJ: image origin center byres :199-231 familiar
ERROR in tokenize(): wrong syntax
I am a bit new to ptraj, so I am not able to understand what is meant by
this error? Is it not able to see end of file or is there problem due to
CHARMM read in file as max frames is read as 0.
Please help me.. Thanks in advance.
Regards
Monika
--
((¯`·_.·[Monika]·._·´¯))
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 25 2010 - 04:30:02 PST
