> For easy reference I'm adding the latest script:
>
> trajin prod_2ns.mdcrd.gz
> trajin prod_4ns.mdcrd.gz
> trajin prod_6ns.mdcrd.gz
> trajin prod_8ns.mdcrd.gz
> trajin prod_10ns.mdcrd.gz
> strip :WAT
> strip :Na+
> trajout test-out representative pdb average pdb averagelinkage \
> clusters 5 mass rms :1-125 .CA
"trajout" does not cluster; it outputs trajectories. You want "cluster"
as per the previous e-mail and your earlier script...
> > cluster out test-out representative pdb average pdb averagelinkage \
> > clusters 5 mass rms :1-125 .CA
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Received on Thu Jun 02 2011 - 07:30:02 PDT
