***  Gap_ranked0  ***
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 = 2206061046261149.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 2206061046261149.atom to be opened.
Openam> File opened: 2206061046261149.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 = 218
First residue number = 1524
Last residue number = 1755
Number of atoms found = 1761
Mean number per residue = 8.1
Pdbmat> Coordinate statistics:
= 366.465704 +/- 10.174936 From: 342.669000 To: 389.050000
= 336.686965 +/- 13.735459 From: 311.452000 To: 369.587000
= 356.132943 +/- 8.947154 From: 335.007000 To: 378.165000
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: SER 1524 N and 2: SER 1524 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: October 18th, 2018.
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