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

From: Prasanth G, Research Scholar <prasanthghanta.sssihl.edu.in>
Date: Sat, 27 Jun 2020 14:59:21 +0530

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

--
parm comdry.prmtop
trajin production_no_wat_ions.nc
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 Sat Jun 27 2020 - 02:30:03 PDT