Interpreting DOT output

Along with the minimum total energy value for each grid point, DOT prints out the file containing the best electrostatic energy, the best solvent excluded volume, and the best total energy value for each processed orientation of the moving molecule.

This file (extension "*.log0.000") has the following format:

    value X Y Z theta phi psi type tag1 value1 tag2 value2 

where "value" is the numerical value of the best energy of the type specified by a "type" keyword. The "type" keywords are:

The fields "value1" and "value2" contain the corresponding best values of energy with the type specified by "tag1" and "tag2" tags. The tag "e=" stands for the electrostatic energy, "n=" - for the solvent excluded volume, and "g=" - for the total energy at the given orientation. This orientation is represented by Eulerian angles: theta phi psi. The position of the moving molecule is determined by the X Y Z coordinates of its center. The following example shows the orientation projection output for two orientations:

    -13.5812 -22   6  -3  0.298  1.416 -0.984 electro n=  -3.9999 g= -17.5812
     -4.0010  15   9  30  0.298  1.416 -0.984 bump e=  -0.6468 g=  -4.6479
    -17.5812 -22   6  -3  0.298  1.416 -0.984 goodness e= -13.5812 n=  -3.9999
    -13.8667  10   8   6  0.298 -2.157  1.725 electro n=  -3.9999 g= -17.8666
     -4.0012 -11  15  14  0.298 -2.157  1.725 bump e=  -0.5909 g=  -4.5921
    -17.8666  10   8   6  0.298 -2.157  1.725 goodness e= -13.8667 n=  -3.9999

The first orientaion (theta = 0.298, phi = 1.416, psi = -0.984) gives the best electrostatic energy (type = "electro") -13.5812 at grid point (-22, 6, -3), with the corresponding best total energy (tag "g=") equal to -17.5812, and the best solvent excluded volume -3.9999.

The second line has the value of the best solvent excluded volume (-4.0010) in its first column (type = "bump") at position (15, 9, 30), and the best values of the electrostatic energy (tag "e=") and the total energy (tag "g=") at this position are -0.6468 and -4.6479.

A utility program "extr" is provided, which extracts the electrostatic energy, the solvent excluded volume, and the total energy values, along with the corresponding positions and orientations from a "*.log0.*" files. extr generates three files: the first file (extension ".bump") contains the solvent excluded volume for each orientation, the second (extension ".electro") contains the electrostatic energy, and the third (extension ".goodness") contains the total energy values.

To run extr, use

    extr base_name

A convenient way to look at the distribution of the best positions and orientations is to sort the *.bump and *.electro files with

    sort -n base_name.bump > base_name.bump.sort
    sort -n base_name.electro > base_name.electro.sort

These sorted results can be further reduced to locate the positions and orientations that have desirable values of both the solvent excluded volume and the electrostatic energy.

For example, to find the 300 best bump values sorted by the corresponding electrostatic energies, use

    head -300 base_name.bump.sort | sort -n +9 > base_name.bump.sort.electro

As another example, to find the 300 best electrostatic energy values sorted by the corresponding solvent excluded volume values, use

    head -300 base_name.electro.sort | sort -n +9 > base_name.electro.sort.bump