On 1/15/17 12:59 AM, abhisek Mondal wrote:
I think I would prefer 'pull-vector' approach given my system's property. Do we have any program to calculate this COM difference and formulate a pull-path ? Can you please give me any paper where this process is used/explained in detail ? I have seen you paper in JPC B but I guess protein-ligand gives a different scenario. Ligands generally found to be trapped in a complex manner inside protein's binding cleft.
Thus you have to figure out the appropriate path for the ligand to exit based on the geometry of the protein. If there's a clear exit channel, compute the COM of, e.g. residues interacting the the ligand and those defining the exit of the channel. The vector is simply the distance between those two COM positions, so you don't need a program, you need a four-function calculator :)
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