Re: [AMBER] RMSD mask selection and closestwater clarification

From: Daniel Roe <>
Date: Thu, 15 Nov 2018 08:12:01 -0500


On Tue, Nov 13, 2018 at 5:17 PM Korey M Reid <> wrote:
> The selection I made was "(:1-294<:5.0)&:WAT.O".

One point here: the mask selection character for "atom" in Amber
syntax is "." (at), not "." (period).

> I am trying to calculate the rmsd of individual water molecules nearest the protein surface to extract residue numbers for each water with an RMSD below a threshold, say 2.5Angs.

I just want to make sure I understand what you are trying to do. You
want to track water molecules that start near some surface. There are
a few things to keep in mind here:

1) All actions (with the exception of 'mask') do not update
distance-based masks on a per-frame basis; they use the active
reference structure to determine what satisfies the given distance
criterion (this is described more in the manual in the Distance-based
masks section).

2) The 'closest' command will reorder the waters by how close they are
to the selected solute region.

The closest command will print out both molecule and atom numbers for
the selected closest waters each frame, e.g.:

#CL[Frame] CL[Mol] CL[Dist] CL[FirstAtm]
           1 1560 1.8259 4895
           1 523 1.8780 1784
           1 527 1.9439 1796

You can select by molecule in recent versions of cpptraj using the "^"
(caret) character.


If you want to exclude everything but the water after a 'closest'
command you can follow with a 'strip' command:

closestwaters 300 ":1-294" closestout closewater.dat name closestwater
strip !:WAT outprefix closestwater

Hope this helps,


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Received on Thu Nov 15 2018 - 05:30:02 PST
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