Hi,
As noted in the cpptraj section of the Amber 17 manual that discusses
distance-based masks (section 28.2.2 Atom Mask Selection Syntax, page
556):
There are two very important things to keep in mind when using
distance based masks:
1. Distance-based masks that update each frame are currently only
supported by the mask action.
2. Selection by distance for everything but the mask action requires
defining a reference frame with reference;
distances are then calculated using the specified reference frame
only. This reference frame can be changed
using the activeref command.
So either use a different reference structure or specify you want
residue 133 via the atom mask expression.
-Dan
On Mon, Sep 11, 2017 at 4:11 AM, colvin <colvin4367.gmail.com> wrote:
> Dear all,
>
> I am trying to compute rmsf for residues with 5 Angstroms from residue 172.
> But the output that I obtained does not include residue 133 in the list.
> Although I'm quite sure that 133 is within 5A from 172, I compute the
> distance between these two residues. The residues 133 distance from 172 is
> ranging from 4-7 Angtroms, for a total of 1000 frames. I then increased the
> distance value for the rmsf value to <8, and still I cannot get 133 in the
> output list.
>
> I'm not sure why this is happening, pls enlighten me.
>
> The commands that I used are:
>
> atomicfluct out rmsfluct_activesite :172<:8.0 byres
>
> distance dist_test :172 :133 out distance_172to133
>
> Thanks!
> _______________________________________________
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Sep 11 2017 - 06:30:07 PDT
