Having seen the AMBER List message (
http://archive.ambermd.org/201103/0813.html)
I modified the the last line of the ptraj.in script changing "clusters 5" for "epsilon 5.0"
The output now is 200 test-out files, and no clustering.
The following WARNINGS were issued by ptraj
WARNING in dispatchToken: Token string "epsilon" not found in tokenlist
WARNING in dispatchToken: Token string "2.0" not found in tokenlist
WARNING in dispatchToken: Token string "mass" not found in tokenlist
I'm at a loss with this one,
Thanks in advance for any help
George
On Jun 2, 2011, at 2:45 PM, George Tzotzos wrote:
> 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 - 06:30:02 PDT
