VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Feb 21 2012 - 02:17:37 CST

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

Well, your psf has 3024 atoms and the dcd 26230 atoms. Did you create the
psf of just the protein instead of the whole system?

-Ajasja

On Tue, Feb 21, 2012 at 07:53, <abinayar_at_imsc.res.in> wrote:

> 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
>
>
>
>
>