Hi there is no keyword for *representative* or *pdb*.
If you want to get representative, please use *repout* command
trajin Apo_aMD_100_300ns.crd.gz
cluster out testcluster *repout mypdb* \
avgout MyAvg.pdb avgfmt pdb \
averagelinkage clusters 10 rms .CA sieve 10
You should expect to see *mypdb.*.crd* files for representative structures.
Hai
On Tue, Jun 28, 2016 at 4:59 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi
>
> I am trying to run cpptraj for cluster analysis
>
> Script that I am following is
>
>
>
> trajin Apo_aMD_100_300ns.crd.gz
> cluster out testcluster representative pdb \
> avgout MyAvg.pdb avgfmt pdb \
> averagelinkage clusters 10 rms .CA sieve 10
>
> But all the time I am getting an error
>
>
> Error: [cluster] Not all arguments handled: [ pdb ]
>
>
> But when I am running same script by removing pdb
>
> trajin PRMT7_Apo_aMD_100_300ns.crd.gz
> cluster out testcluster representative \
> avgout MyAvg.pdb avgfmt \
> averagelinkage clusters 10 rms .CA sieve 10
>
>
> it seems to be running.
>
> I want to know that I am on correct path or not?
>
>
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Received on Tue Jun 28 2016 - 14:30:02 PDT
