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Generate the most probable trajectory between two states
The program will output, in addition to the trajectory in PyMOL format, the coordinates of the transition state as well as the total action Stot and the energy of the transition state UL (measured with respect to the energy of the left -initial- state).
Q1 and Q2 will also be found in the logfile, where Q1 is the number
of contacts as in the initial state, and Q2 the number of contacts
as in the final state, for each point along the trajectory.
Here is an example (adenylate kinase), where the trajectory obtained with UMMS is also presented.
If needed, a Q1-specific - Q2-specific vs Q-common plot can be built upon request. This kind of plot reveals possible unfolding during the transition (see Okasaki et al., 2006).
The Elastic Energy during the transition
could be calculated upon request.
The attached plot
demonstrates that MinActionPath generates a trajectory with
less elastic energy than UMMS linearly interpolated one
(see curve pink+green vs blue+red curve).
This again concernes adenylate kinase with elastic spring constants of 0.1 kcal/Mol/Å2 for both sides.
Finally, the question of the robustness of the trajectory with respect of the k1/k2 ratio, i.e. the elastic constants for both sides of the reaction, is of interest. Here is a Q1 vs Q2 plot for adenylate kinase and k2/k1 = 5, k1 = k2 and k1/k2 = 2.
An ASCII file ('something_overlap.out') will be generated.
The first column corresponds to the frame number along the trajectory.
The 106 following columns correspond, in ascending order, to the
overlap between the set of difference vectors (with respect to
the starting structure) and the N first normal modes
(N=1,106, also calculated from the starting structure).
The 6 first columns must always have negligible values compared to the 7th.
A PDB file ('something_pseudophi.pdb') will be generated.
It corresponds to the PDB file of the end structure where
the B-factor column is replaced with the pseudo-'phi value'.
This allows for direct visualisation using either PyMOL or VMD.
To make a long story short, here we monitor the elastic energy of each residue (through its Calpha) along the trajectory. The 'time' at which this local elastic energy is maximal corresponds to its own 'transition time'. This is what is stored in the B-column. Comparing this value to the global transition time will tell you whether this residue has a early or late transition. Other definitions of residue-specific transition time(s) are described in Zhu and Hummer (2009), Biophys. J. 97:2456-63.