From: abinayar_at_imsc.res.in
Date: Tue Feb 21 2012 - 00:53:08 CST

  Dear VMD users,

I am trying to perform rmsd calculations throught Tcl scripts. My protein
is solvated.First of all,I obatined the .psf file of my protein from
.prmtop AMBER file.
Then using Tcl scripts , I obtained .psf file of my protein crystal
(fitting frames).
After this, when I ran my script for rmsd analysis,I obatined the
following error:
psfplugin) WARNING: no angles defined in PSF file.
psfplugin) WARNING: no dihedrals defined in PSF file.
psfplugin) WARNING: no impropers defined in PSF file.
psfplugin) no cross-terms defined in PSF file.
Info) Analyzing structure ...
Info) Atoms: 3024
Info) Bonds: 3058
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 188
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 1 Nucleic: 0
0
ERROR) Error reading optional structure information from coordinate file
2d7j_crystal.pdb
ERROR) Will ignore structure information in this file.
Info) Using plugin pdb for coordinates from file 2d7j_crystal.pdb
ERROR) Incorrect number of atoms (1550) in
ERROR) coordinate file 2d7j_crystal.pdb
Info) Finished with coordinate file 2d7j_crystal.pdb.
0
Info) Using plugin psf for structure file 2d7j_crystal.psf
psfplugin) WARNING: no angles defined in PSF file.
psfplugin) WARNING: no dihedrals defined in PSF file.
psfplugin) WARNING: no impropers defined in PSF file.
psfplugin) no cross-terms defined in PSF file.
Info) Analyzing structure ...
Info) Atoms: 3024
Info) Bonds: 3058
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 188
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 1 Nucleic: 0
1
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
ERROR) BaseMolecule: attempt to init atoms while structure building in
progress!
ERROR) Invalid number of atoms in file: 26230
Info) Using plugin dcd for coordinates from file gmpase-run1.dcd
ERROR) Incorrect number of atoms (26230) in
ERROR) coordinate file gmpase-run1.dcd
Info) Finished with coordinate file gmpase-run1.dcd.
1

Kindly let me know the reason for this error. What is the reason for
missing co-ordinates?

Thanking you,
Yours sincerely,
Abinaya