Re: [AMBER] Error: [cluster] Not all arguments handled: [ pdb ]

From: Thakur, Abhishek <axt651.miami.edu>
Date: Tue, 28 Jun 2016 21:36:32 +0000

Thank you

Just now I have run it and it worked.

________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: Tuesday, June 28, 2016 10:07:54 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Error: [cluster] Not all arguments handled: [ pdb ]

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 - 15:00:02 PDT