AMBER Archive (2009)

Subject: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis

From: Cenk \(Jenk\) Andac (cenk_andac_at_yahoo.com)
Date: Fri Oct 16 2009 - 07:19:24 CDT

Dear AMBER community,
 
I have been working on a non-competitive enzyme reaction in explicit water media by QM/MM. I have run 4 ns of QM/MM for a enzyme system including cofactors and a ligand. I have implemented MMTSB cluster analysis for residues 1-84 of the protein (excluding the cofactors and the ligand), and now I would like to compare the MMTSB clusters to ptraj clusters.However, I can't seem to get the ptraj's cluster function working as it appears below:
 
trajin enzyme.qmmm.traj
cluster out reductase representative pdb average pdb means clusters 5 rms :1-84  
 
 
The error message I get is "segmentation fault".
 
I would appreciate it if someone tells me what I am doing wrong.
 
best regards,
 
Jenk  
 
 
 

      
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