Re: [AMBER] Ligand movement w.r.t protein backbone

From: Debarati DasGupta <>
Date: Mon, 29 Jun 2020 16:24:30 +0000

Hello Daniel,
So if you may help me in understanding whats the difference in the 2 RMSD txt files I generate here! SO I get 2 outputs as can be seen namely backbond_aligned_RMSD.txt and lig_probb_rmsd.txt. SO what is the difference in outputs I get from them?
Its funny that I wrote the input file and then I am a bit lost as to what data gets generated
I am trying to monitor the movement of my ligand (IPA) wrt the protein backbone in a 20ns trajectory.

parm post_processed_IPA_solvated.prmtop
trajin post_processed_IPA_solvated_prod.mdcrd 1 last
center mass origin :1-287
image origin center
reference post_processed_IPA_solvated_box_SITE1.pdb
strip :WAT
strip :Na+
rms reference mass out backbond_aligned_RMSD.txt :3-286.CA,C,N,O
rms IPA_site1 :IPA&!.H= nofit mass out lig_probb_rmsd.txt

From: Daniel Roe<>
Sent: 29 June 2020 12:07
To: AMBER Mailing List<>
Subject: Re: [AMBER] Ligand movement w.r.t protein backbone


On Sat, Jun 27, 2020 at 5:29 AM Prasanth G, Research Scholar
<> wrote:
> Dear all,
> I would like to compute the RMSD of ligand w.r.t the backbone of protein
> during the simulation. Can you please suggest if this cpptraj script will
> give me the intended result

Not exactly; this will just give the RMSD with respect to the ligands
position in the first frame. You should first fit on the protein, then
do 'nofit' RMSD on the ligand (so that it's actually calculated in the
reference frame of the protein). So e.g. (assuming your protein is
molecule 1):

rms Protein ^1.C,CA,N mass
rms rms1 :LIG&!.H= nofit mass out results/lig_probb_rmsd.dat

Hope this helps,


> --
> parm comdry.prmtop
> trajin
> rmsd rms1 ":LIG&!(.H=)" nofit mass out results/lig_probb_rmsd.dat
> go
> clear all
> quit
> --
> I felt this script gives the rmsd of ligand w.r.t protein. Can you please
> suggest a solution.
> Thank you.
> --
> Regards,
> Prasanth.
> _______________________________________________
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Received on Mon Jun 29 2020 - 09:30:06 PDT
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