Should you encounter any unexpected behaviour,
please let us know.

STDOUT:

CUTOFF set to default value (CUTOFF=8)
Build Tirion matrix:
 Pdbmat> Computes the Hessian matrix, using an Elastic Network Model.
 Pdbmat> Version 3.50, Fevrier 2004.    

 Pdbmat> Options to be read in pdbmat.dat file.

 Pdbmat> Coordinate filename     = 2406090513311877134.atom

 Pdbmat> Distance cutoff         =       8.00
         Force constant          =      10.00
         Origin of mass values   =       CONS
 Pdbmat> Levelshift              =    1.0E-09
         PRINTing level          =          2

 Pdbmat> Coordinate file 2406090513311877134.atom to be opened.

 Openam> File opened: 2406090513311877134.atom

 Pdbmat> Coordinate file in PDB format.

 Rdatompdb> Reading pdb file.
 Rdatompdb> End of file reached.
 Rdatompdb> Number of I/O errors:      0

 Rdatompdb> Number of residues found =    320
            First residue number     =      2
            Last  residue number     =     26
            Number of atoms found    =   3897
            Mean number per residue  =     12.2

 Pdbmat> Coordinate statistics: 
 =    63.109663 +/-    16.731527 From:    27.621000 To:    99.895000
 =    -5.246310 +/-    14.459788 From:   -41.236000 To:    29.594000
 =   -16.329000 +/-    11.967712 From:   -44.578000 To:     6.381000
 Pdbmat> Masses are all set to one.
%Pdbmat-W> residue:'DT  ' is not a well known amino-acid.
%Pdbmat-W> residue:'DG  ' is not a well known amino-acid.
%Pdbmat-W> residue:'DA  ' is not a well known amino-acid.
%Pdbmat-W> residue:'DC  ' is not a well known amino-acid.
%Pdbmat-W> residue:'DC  ' is not a well known amino-acid.
%Pdbmat-W> residue:'DT  ' is not a well known amino-acid.
%Pdbmat-W> residue:'DT  ' is not a well known amino-acid.
%Pdbmat-W> residue:'DC  ' is not a well known amino-acid.
%Pdbmat-W> residue:'DC  ' is not a well known amino-acid.
%Pdbmat-W> ........

%Pdbmat-W>    104 residue(s) not known.

 Openam> File opened: pdbmat.xyzm
 Pdbmat> Coordinates and masses considered are saved.

 Openam> File opened: pdbmat.sdijb

%Pdbmat-Er> Too small distance =  0.000     between following atoms.
  1817: DA       3 P    and   2877: DA       3 P   
%Pdbmat-Er> Too small distance =  0.000     between following atoms.

 ***   pdbmat failed for the reason given above     **** 
 ***   please check your input file and parameters  **** 
 ***   (are there two atoms at the same position?   **** 
 ***    e.g. alternative conformations )            **** 



STDERR:
STOP *Wrong coordinates*

• K. Suhre & Y.H. Sanejouand, ElNemo: a normal mode web-server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Research, 32, W610-W614, 2004.
• K. Suhre & Y.H. Sanejouand, On the potential of normal mode analysis for solving difficult molecular replacement problems. Acta Cryst. D vol.60, p796-799, 2004 © International Union of Crystallography.