[gmx-users] question on g_cluster

[Osman Yogurtcu]

Hi,
 
Is it possible to use g_cluster to cluster NAMD2 trajectories?
 
I am trying to use g_cluster to cluster my NAMD2 deriven trajectories. First, I converted my .dcd trajectory into .pdb format. Then, tried this:  
 
>g_cluster -f mypdb.pdb -cl clusters.pdb
 
and it did not work. Later, I converted my .pdb to .xtc and tried: 
 
>g_cluster -f myxtc.xtc -cl clusters.pdb
 
does not work either. Should I include a Gromacs MD run specific .tpr topology file as well, though it is mentioned as "optional input"?
 
I hope you can help me out,
 
Best
 
Osman N. Yogurtcu

Center for Computational Biology and Bioinformatics 
Research Assistant 
Koc University 
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