Job Title:
1vom

Cutoff distances for building ENM:
Rc(aa-aa)=10.0
Rc(aa-dntp)=12.5
Rc(dntp-dntp)=15.0

A coarse-grained representation (2 residues per ENM node) is used here.

Conformational change from PDB1 to PDB2: RMSD = 5.09 (for 730 residues)

Normal mode analysis for the PDB1:

TABLE: Lowest 10 non-zero global modes (excluding 6 zero modes)

mode #	eigenvalue	collectivity	deformed model
G#6	0.003315	0.085	PDB file(+) (movie), PDB file(-) (movie)
G#7	0.005970	0.079	PDB file(+) (movie), PDB file(-) (movie)
G#8	0.006383	0.078	PDB file(+) (movie), PDB file(-) (movie)
G#9	0.010045	0.021	PDB file(+) (movie), PDB file(-) (movie)
G#10	0.010607	0.009	PDB file(+) (movie), PDB file(-) (movie)
G#11	0.012864	0.331	PDB file(+) (movie), PDB file(-) (movie)
G#12	0.015383	0.120	PDB file(+) (movie), PDB file(-) (movie)
G#13	0.017479	0.310	PDB file(+) (movie), PDB file(-) (movie)
G#14	0.021305	0.229	PDB file(+) (movie), PDB file(-) (movie)
G#15	0.023867	0.144	PDB file(+) (movie), PDB file(-) (movie)

Transition paths:

The SP (Saddle Point) path: download PDB file (view movie) (the SP of the MENM potential is at frame 14 and the SP path has 25 frames).
The overlap value for each of the lowest 10 modes along the SP path is plotted here, which shows how much each mode contributes to the transition.
Note: the SP path is traced by the SP as the MENM parameters (mixing temperature and energy offset) are varied.

The SD (Steepest Descent) path: download PDB file (view movie) (the SP of the MENM potential is at frame 13 and the SD path has 24 frames).
The overlap value for each of the lowest 10 modes along the SD path is plotted here, which shows how much each mode contributes to the transition.
Note: the SD path is obtained by starting from the SP and following the negative gradient of the MENM potential toward both end-state structures.