Normal mode analysis TSD Journal

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Input

PDB file 2gk1 was used as input. Chain A was extracted and two files prepared, one containing only the protein part and one also containing the ligand NGT as ATOMs (instead of HETATMs). All other HETATMs were removed in both cases.

elNemo

elNomo was run at the respective webserver at default parameters except that the cutoff for elastic interactions was increased to 10 from the default 8.

createPNGs.pml will perform every necessary task inside Pymol to create a PNG for every frame of the animation. createAnimations.sh will create the final animated gif from these PNGs.