Generating the trajectory with minimum action between two conformational states of large macromolecular complexes
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About this program
This is an updated version of MinActionPath
that generates the transition path between two known conformational states of the same macromolecular complex.
It differs from existing morphing techniques by using the principle of least action
(see also Ref.).
It can now handle very large data files and offers different ways to define the energy landscape (ENM or Go-like)
and the neighbours (through a cutoff or by using Delaunay tessalation) in the pair-wise energy terms.
The program can process structures with a very large number of residues (e.g. 100,000) usually represented
in a coarse-grained fashion with one atom (bead) per residue (usually the C-alpha).
It features an energy landscape based on the Elastic Network Model (ENM) or on the Go Model,
Using the Go Model, there will be less deformations of the backbone of the proteins during the transition path,
i.e. the geometry of the chain will be more preserved than with the ENM.
It also proposes a definition of neighbours using Delaunay tessalation as described
Using this method, the calculation will be more rapid (there are less neighbours per site)
and unwanted "dangling effects" of loosely connected domains will be avoided.
More on the Go-model:
It is designed in a such a way that the stereochemistry of proteins
will be deformed minimally during the transition
through the addition of several two-body energy terms :
the bond length term, two elastic terms based on torsional
and dihedral angles, and a non-local-term (vdw-like).
This form helps you to specify the two PDB input files and the parameters of the simulation.
You need two files (in PDB or CIF format) for the initial and final states of the transition you want to calculate.
The two structures need not to have been aligned beforehand, the program will do it anyway.
If the number of residues in the two files are different, the algorithm will attempt to match them
and will work only with the common atoms. This is also true if there are different chains.
Energy can be as in the Elastic Network Model or as in the Go Model.
Neighbours in the two-body energy terms can be defined either with a cutoff (in Angstrom) or by Delaunay tessalation (no cutoff).
In the form itself, information on the fields that are to be filled in are contained in the blue "information" icon next to it.
The output files are the trajectory ("trajectory.cif") and the coordinates of the transition state ("transition.cif").
In the logfile ("output.txt") you will find details on the progression of the algorithm, in particular in its search of the transition state.