***  1PC3  ***
output from eigenvector calculation:
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 = 240228061418940321.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 240228061418940321.atom to be opened.
Openam> File opened: 240228061418940321.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 = 369
First residue number = 19
Last residue number = 54
Number of atoms found = 2696
Mean number per residue = 7.3
Pdbmat> Coordinate statistics:
= 86.112928 +/- 16.242217 From: 0.000000 To: 120.233000
= 23.039867 +/- 8.158674 From: 0.000000 To: 43.319000
= 0.463957 +/- 8.458975 From: -19.544000 To: 25.141000
Pdbmat> Masses are all set to one.
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.
1: VAL 19 N and 2425: VAL 19 N
%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*
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elNémo
is maintained by Yves-Henri Sanejouand.
It was developed
by Karsten Suhre.
Between 2003 and 2014, it was hosted by IGS (Marseille).
Last modification: April 25th, 2023.
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