[AMBER] Clustering using CPPTRAJ

From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
Date: Mon, 23 Jun 2014 15:51:15 +0200

Dear Amberists;

I have a tricky issue.

 I have a 50ns MD trajectory (50000 frames) and I would like to cluster the
frames based on an RMSD cutoff value from a reference structure. For
example, I need to cluster the frames (structures) that exist within RMSD
value of 1.0 A of a reference structure.

Is there anyway to know the corresponding frame numbers which belongs to a
RMSD cutoff 1.0 A or even extract those frames.

I know there is an option n CPPTRAj to do that

Script looks like

trajin *md1.mdcrd*
rms R1 first :1-198 .CA
outtraj frames_rms1_md1.mdcrd maxmin R1 min 0.0 max 1.0

Please suggest if this script looks good for this process. And any way to
calculated binding free energy on these extracted frames.

Help and suggestion regarding this will be highly appreciated.

Thanks & Regards;
Soumendranath Bhakat
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Received on Mon Jun 23 2014 - 07:00:02 PDT
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