[gmx-users] question on g_cluster

[David van der Spoel]

Osman Yogurtcu wrote:
> 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,
>  


try using -s reference.pdb

> Best
>  
> Osman N. Yogurtcu
> Center for Computational Biology and Bioinformatics
> Research Assistant
> Koc University
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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