[AMBER] CPPTRAJ - Filtering frames based on lowest of the two RMSD values

From: Stevens, David <david.stevens.richmond.edu>
Date: Mon, 20 Jul 2015 18:30:00 -0400

To whom this concerns,

    I am trying to figure out a way to specify and filter frames between
two different conformations of my protein. I would like to create a new
trajectory file of only the closed conformation and another one of only the
semi-open. I have two crystal structures that I am referencing and
performing an RMSD calculation against with a 2.5 Angstrom cutoff. I
would like any frames that do not meet the 2.5 Angstrom criteria for either
of the crystal structures to not be included into either of my new
trajectories (If it could turn into a third trajectory, that would be

  The difficulty that I am running into is that there are some frames in my
original trajectory that have an RMSD of lower than 2.5 for both
conformations. In this case I would like the frame to be "binned" into the
new trajectory that has the lowest RMSD.

Ex: Frame 733 has an RMSD value of 2.1 for closed and 1.4 for
semi-open. In this case, I would like a binning to the lowest RMSD to
occur and Frame 733 to be put into the new trajectory for the semi-open

   I have used the Filter command for cpptraj before, but only to specify
what frames I want based on a single comparison of RMSD. In this case,
there are two RMSD comparisons occurring at the same time and I have not
been able to figure out a way to make this happen.

Below is my cpptraj input:

*trajin Combined_ALL_Traj.pdb *

*reference /home/ds9ug/pdb/closed_backbone.pdb [xtal]*

*rmsd closed :45-55,79-82.CA,N,C bound 0 bound 2.5 ref [xtal]*

*reference /home/ds9ug/pdb/semiopen_backbone.pdb [xtal]*

*rmsd semiopen :45-55,79-82.CA,N,C bound 0 bound 2.5 ref [xtal]*

*#distance dist :50.CA :149.CA *

*#filter dist min 12 max 46 out filter.dat *

*filter rmsd min 0 max 2.5 filter_rmsd.dat*

*trajout semi_open_filtered.pdb pdb*

Any help would be fantastic.

Thank you,

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Received on Mon Jul 20 2015 - 16:00:02 PDT
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