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

From: Prasanth G, Research Scholar <>
Date: Mon, 29 Jun 2020 23:06:38 +0530

Hello Daniel,
Thank you for the response. I modified the script according to your
One more request. Let me know if the command for obtaining histogram
representation of this data is correct or not.
P.S: the result looks more meaningful after this alteration.
*>parm comdry.prmtop  *
*                 > trajin
*> rms :1-670.C,CA,N mass*
    RMSD: (:1-670.C,CA,N), reference is first frame (:1-670.C,CA,N),
Best-fit RMSD will be calculated, coords will be rotated and translated.
*> rms rms1 :671&!.H= nofit mass out results/Lig_probb_rmsd_50.dat*
RMSD: (:671&!.H*), reference is first frame (:671&!.H*), mass-weighted.
No fitting will be performed.
> *histogram rms1,*,*,.1,* norm out results/Lig_pro_rmsd_nofit_hist.dat*
Hist: results/Lig_pro_rmsd_nofit_hist.dat: Set up for 1 dimensions using
the following datasets:
[ rms1 ]
norm: Sum over bins will be normalized to 1.0.
*> go*
Thank you!
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Received on Mon Jun 29 2020 - 11:00:03 PDT
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