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

From: Daniel Roe <>
Date: Mon, 29 Jun 2020 12:07:27 -0400


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 - 09:30:04 PDT
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