Re: [AMBER] Clustering using CPPTRAJ

From: Jason Swails <>
Date: Mon, 23 Jun 2014 15:35:25 -0400

On Tue, 2014-06-24 at 00:38 +0530, Soumendranath Bhakat wrote:
> Dear Jason;
> Say I extract the trajectory with frames below RMSD 1 Ang. from the
> reference structure using this
> trajin *md1.mdcrd*
> rms R1 first :1-198 .CA
> outtraj frames_rms1_md1.mdcrd maxmin R1 min 0.0 max 1.0
> Say now I have frames_rms1_md1.mdcrd. How can I process this
> frames_rms1_md1.mdcrd file for MMGBSA/MMPBSA and how can I define frames in
> this case. Also frames_rms1_md1.mdcrd contins trimmed trajectories within
> RMSD 1 Ang.. So if I want to process this trajectory how can I process it
> for mmpbsa or gbsa. How an input file will look like in this case.

frames_rms1_md1.mdcrd will only contain frames that satisfy the minimum
or maximum RMSD. Suppose md1.mdcrd has 100 frames, and 48 of them have
an RMSD below 1 Angstrom. In this case, frames_rms1_md1.mdcrd will have
48 frames in the same order as they appear relative to each other in

Then apply the logic I described in my last email to this 48-frame,
filtered trajectory file.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 23 2014 - 13:00:02 PDT
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