Re: [AMBER] RMSD for two different MDs

From: Daniel Roe <>
Date: Tue, 29 Nov 2016 08:34:07 -0500


Since you want to compare two different ligands to each other, you'll
need a common reference structure (as Dave Cerutti suggested). This
could be e.g. the conformation of one of the ligands in a crystal
structure, etc. Then what I would do for each trajectory is first
rms-fit the protein, then take the no-fit RMSD of the ligand atoms you
have in common. So say for example your protein is residues 1 to 56,
your first ligand is phenylalanine, and your second ligand is
tyrosine. The atoms in common are everything except OH and HH for Tyr
and HZ for PHE. Your input could be something like:

parm Protein-Tyr.parm7
reference Protein-Tyr.crystal.pdb parm Protein-Tyr.parm7
trajin parm Protein-Tyr.parm7
# Fit the protein to reference
rms reference :1-56
# No-fit RMSD of common Tyr ligand atoms
rms Tyr reference nofit :57&!.OH,HH,HZ out rmsd.agr
# First pass
# Clear first trajectory
clear trajin
# Load second topology and trajectory
parm Protein-Phe.parm7
trajin parm Protein-Phe.parm7
# Again fit protein to reference
rms reference :1-56
# No-fit RMSD of common Phe ligand atoms
rms Phe reference nofit :57&!.OH,HH,HZ out rmsd.agr
# Second pass

Depending on what atoms are actually in common you may need or want to
specify a second mask to RMSD to specify what atoms in the reference
should match up to target. The 'select' command can be useful in
diagnosing issues with atom selection. Hope this helps,


On Mon, Nov 28, 2016 at 3:49 PM, Haining Liu <> wrote:
> Hi Amber list,
> I want to compare the RMSD of two different ligands in the same protein to
> find out whether they have similar binding. Specifically, I have
> protein + ligand 1 (50 ns MD)
> protein + ligand 2 (50 ns MD)
> ligand 1 and ligand 2 structurally different, but similar. I want to get
> the RMSD of ligand 1 and ligand 2 in each of the 50 ns snapshot. Is there a
> way to do this by cpptraj?
> Thank you very much for your help.
> Haining
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Tue Nov 29 2016 - 06:00:02 PST
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