Re: [AMBER] RMSD mask selection and closestwater clarification

From: Korey M Reid <>
Date: Thu, 15 Nov 2018 22:18:28 +0000

Hello Dan,
Thank you for the clarification on the selection, I found that syntax in a discussion about distance selection and I had been confused but my efforts to use just "(:1-N<:R)&:WAT" was not working either,which, I had assumed that this may have been an issue with less than all three atoms being within the cutoff, so I attempted things lastly including the syntax I reported; I am grateful. With this syntax, "(:1-N<:R)&:WAT", will I select all atoms belonging to a WAT molecules if one or more atoms are within the cutoff, or is it limited to the atoms within the cutoff from any protein residue in my system? I am under the impression that it will do the later, only select atoms within the cutoff. I have not successfully used that syntax to return any water molecules within that distance, instead if I use the syntax, "(:k<:R):&:WAT", I get back the single residue k and all waters within R, which is great but adds the necessity of a for loop and some post processing to get all the water residues saved and whole, at t
he moment I run a for loop over k and I select for :WAT.O, following your response of course, and have to use a python script to create an array of unique waters. I would like to avoid this since checking my systems is cumbersome at 300x150ps NVE trajectories.
To follow up 1) I am forcing the mask to only operate on the first frame, for my analysis I want only the waters that are present within a certain radius from the surface and mostly isolated to a specific region so I can compare these bound waters to others with similar relative dynamics. Thank you for clarifying the usage of closest waters also, this is very enlightening with respect to injecting the output into the strip command which looks promising.

Thank you and with best,

From: Daniel Roe <>
Sent: Thursday, November 15, 2018 5:12 AM
To: AMBER Mailing List
Subject: Re: [AMBER] RMSD mask selection and closestwater clarification


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 - 14:30:02 PST
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