Difference between revisions of "Energy Scoring Method in Grid"
From Rizzo_Lab
Stonybrook (talk | contribs) |
Stonybrook (talk | contribs) |
||
| Line 1: | Line 1: | ||
The general form of energy scoring function: | The general form of energy scoring function: | ||
| − | [[Image:1.png|thumb|center| | + | [[Image:1.png|thumb|center|500px|Energy scoring function]] |
It's easy to see that the Coulumb potential Energy term could be separated into receptor and ligand part. If the Lennard-Jones one could be separated, it will be easy to precalculate the potential of each grid point in docking region and speed up the docking process. | It's easy to see that the Coulumb potential Energy term could be separated into receptor and ligand part. If the Lennard-Jones one could be separated, it will be easy to precalculate the potential of each grid point in docking region and speed up the docking process. | ||
Computational chemist took the assumption that the coefficients for Lennard-Jones part in energy scoring function are also separable. | Computational chemist took the assumption that the coefficients for Lennard-Jones part in energy scoring function are also separable. | ||
| − | [[Image:2.png|thumb|center| | + | [[Image:2.png|thumb|center|200px|Lennard-Jones coefficients]] |
The new form of energy scoring function like this: | The new form of energy scoring function like this: | ||
| − | [[Image:3.png|thumb|center| | + | [[Image:3.png|thumb|center|450px|Energy score function]] |
So each time, when you run the grid calculation, you get | So each time, when you run the grid calculation, you get | ||
| − | [[Image:4.png|thumb|center| | + | [[Image:4.png|thumb|center|450px|potential energy at each grid point]] |
and Save them in your *.nrg file. | and Save them in your *.nrg file. | ||
Revision as of 13:13, 5 March 2015
The general form of energy scoring function:
It's easy to see that the Coulumb potential Energy term could be separated into receptor and ligand part. If the Lennard-Jones one could be separated, it will be easy to precalculate the potential of each grid point in docking region and speed up the docking process.
Computational chemist took the assumption that the coefficients for Lennard-Jones part in energy scoring function are also separable.
The new form of energy scoring function like this:
So each time, when you run the grid calculation, you get
and Save them in your *.nrg file.
