Hi everybody,
Following the manual instructions, I'm using the following ptraj.in script for clustering
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+
cluster out test-out representative pdb average pdb averagelinkage
clusters 5 mass rms :1-125 .CA
The summary of the output is:
PTRAJ: cluster out test-out representative pdb average pdb averagelinkage
WARNING in ptraj(), cluster: Must specify either 'clusters' or 'epsilon'.
PTRAJ: clusters 5 mass rms :1-125 .CAWARNING in ptraj(), cluster: you need to specify an output file,
i.e. "out cluster" ...ignoring command.
[No output trajectory specified (trajout)]
NO OUTPUT COORDINATE FILE WAS SPECIFIED
Any ideas as to where my script has gone wrong will be greatly appreciated
George
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Received on Thu Jun 02 2011 - 06:00:02 PDT
