Re: [AMBER] RMSD of residues within 3A of ligand

From: Daniel Roe <>
Date: Wed, 1 Dec 2021 11:30:24 -0500


>From the Amber/Cpptraj manual:
Distance-based Masks
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.
The problem with distance-based masks for most commands is that the
number of atoms selected each frame can change, which requires setting
everything up for the new selection which can get expensive. It's
particularly difficult for something like RMSD where the # of atoms
selected in the reference and target need to match in order for the
RMSD to be meaningful. You could script it so that you loop over every
input frame in the trajectory and try to change the active reference
accordingly, but again if you select different #s of atoms in the
target and reference you can't calculate the RMSD anyway.

TL;DR unfortunately, there's no easy way to do what you want.


On Fri, Oct 22, 2021 at 9:57 AM Sadaf Rani <> wrote:
> Dear Amber users
> I want to calculate rmsd of the residues within 3 A of the ligand for which
> I used the following syntax
> rms to first :490<.3 first out rmsd_lig3A.dat
> rms tofirst1:490 first out rmsd_lig3A.dat
> However, I am getting the same curve for both which shows that the syntax
> for 3A has not been taken up by the cpptraj.
> Could you please correct me where I am doing wrong?
> Thanks in advance.
> Regards
> sadaf
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Received on Wed Dec 01 2021 - 09:00:02 PST
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