[AMBER] Removing rotational-transnational movements in dimmer protein

From: Enrico Martinez via AMBER <amber.ambermd.org>
Date: Mon, 13 Feb 2023 15:07:42 +0100

Dear Amber users!

Dealing with the molecular modeling of protein-ligand dimeric complex I am
using the following CPPTRAJ script for post-processing of a MD trajectory:

parm ./protein.prmtop
trajin ./prod_*.netcdf
# center to the resider located in the interface between two monomers
center :7
# strip all solvent
strip :WAT
strip .Na+
strip .Cl-
trajout ./traj55.pdb offset 10 model

It removes jumping of the protein across the PBC and correctly centers the
view. However, it does not remove rotational and translational degrees of
freedom from the protein, so in the resulting trajectory it still may

How could I completely immobilize protein in terms of its global dynamics,
in order that I could focus on the conformational breathing as well as
ligand binding site ?

Many thanks in advance


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Received on Mon Feb 13 2023 - 06:30:02 PST
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