[gmx-users] error in g_cluster "diagonalization" method

[Isaure Chauvot de Beauchêne]

Hi,

I'm trying to cluster 200 structure of a 20 aas peptide, by the  
g_cluster "diagonalization" method. There is my command line:

*********************
g_cluster -f all_1-200.pdb -s ../pdb/FinalGSAFold_1.pdb -clid -cl  
clusters.pdb -method diagonalization -o rmsd-clust.xpm -g cluster.log
*********************

I obtain these lines:

*********************
The RMSD ranges from -nan to -nan nm
Average RMSD is -nan
Number of structures for matrix 200
Energy of the matrix is -nan nm
*********************

If I run exactly the same job with changing for "gromos" method, I obtain:

*********************
The RMSD ranges from 0.26113 to 1.22787 nm
Average RMSD is 0.622773
Number of structures for matrix 200
Energy of the matrix is 41.58 nm
...etc
*********************

Are there some case in which the diagonalization method is not usable?  
What could be the reason of this fail?
I use VERSION 4.5.5.

Thanks a lot in advance,

Isaure

-- 
Dr Isaure Chauvot de Beauchêne
Ph.D student

Team: "Bioinformatics, Modelisation and Molecular Dynamics" (BiMoDyM),  
Dir L. Tchertanov.
LBPA-CNRS, ENS-Cachan, LabEx LERMIT

61 Avenue du Président Wilson
94230 Cachan
FRANCE