[AMBER] cpptraj clustering

From: Neha Gandhi <n.gandhiau.gmail.com>
Date: Thu, 26 Dec 2013 19:03:39 +0800

Dear List,

I have 1 microsecond trajectory and each frame is saved every 10 ps. I
m using following command to perform clustering analysis

trajin prod1.mdcrd 1 1000 1
trajin prodX.mdcrd 1 1000 1
strip :WAT
strip :Cl-
strip :Na+

cluster hieragglo epsilon 4 averagelinkage rms.CA sieve 10 out
cnumvtime summary summaryfile clusterout clus clusterfmt amber repout
repclus repfmt pdb

I get following warning:
Warning: [cluster] Not all arguments handled: [ sieve 10 ]

Is the syntax correct? I am using averagelinkage since I don't know
the total number of clusters in the final outcome. Is the above syntax
doing clustering based on Calpha atoms? Since processing 10000 frames
is time consuming, I thought I would use sieve to use less number of
frames for clustering.

Your guidance is appreciated.

Neha Gandhi

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Received on Thu Dec 26 2013 - 03:30:03 PST
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