Re: [AMBER] cpptraj - atomicfluct

From: Thomas Cheatham <>
Date: Mon, 15 Sep 2014 19:47:37 -0600 (MDT)

> Im trying to calculate B-factors for the backbone CA atoms of selected residues (18-125)
> trajin
> rms first mass out rmsd_first.dat :18-125.CA
> atomicfluct out bfactor.apf .CA byatom bfactor
> Both ptraj and cpptraj produce an output (bfactor.apf) that fails to
> select the residues in the mask. Instead it produces B-factors for all
> residues (1-125).

As mentioned by DAC, .CA in the atomicfluct command selects all CA atoms.
The command doesn't note the context of the fit. If you simply want to
see the data for :18-125, scale what you show in the graphics program
(i.e. do not display :1-17,126-??????

> In addition, the bfactor.apf output in ptraj shows residue numbers
> whereas in cpptraj atom numbers.

The ptraj output just shows numbers for the selection; it does not "parse"
what you are trying to interpret in terms of atoms/residues. You picked
CA, so it is showing CA #1 -> #N.

> Id appreciate any suggestions how to modify the script to select only
> the residues in the mask and additionally to have cpptraj generating an
> output with residue numbers rather than atom numbers

...there is not an easy way to have ptraj/cpptraj output "residue" numbers
as you see fit. It simply outputs x-axis that are numbered 1->N for the
select groups (either byres or bynum, still numbered 1->N based on the
selection and NOT matched to atom/residue numbers).

I think you want what ptraj is outputing based on what your script shows
as written and simply change the x-axis display to only show 18-125.


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Received on Mon Sep 15 2014 - 19:00:02 PDT
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