The DOT Command (.com) file

The example1.com file.

You specify input data to DOT via the DOT command file. Information in this command file includes

• Parameter values
• Input file names

The command file for the supplied example is called example1.com, and is shown below.

    dot_version                     1.0_alpha
    verbose                         2
    autocenter_stl                  true
    autocenter_mov                  true
    saved_best_values               1000
    per_orientation_statistics      4
    per_orientation_stat_thresh     -1000.0
    bumplimit                       200.0
    neighborhood_weight             0.1
    do_energy                       true
    do_partition_sum                true
    temperature                     310.0
    sum_type                        -1
    still_grid_clamp_low            -1.0
    still_grid_clamp_high           1000.0
    pot_grid_clamp_low              -6.0
    pot_grid_clamp_high             6.0
    SizeX                           128
    SizeY                           128
    SizeZ                           128
    gridstep                        1.0
    pot_file                        mache_fas_p2_ts.grd
    stl_m_file                      mache_fas_p2_tsc_2A.vol
    mov_file                        ac10ampac_hs.dot
    rotfile                         30_zero.euler
    outfile                         ac10_hs_mache_fas_p2__2A_0bumps_tst

The information below gives both brief and detailed explanation of all user-defined parameters in the command file. The last four parameters specify input files that must be prepared before running DOT.

Table of Parameters

Description of Parameters

dot_version:

This descriptor indicates which version of DOT the command file is for.

saved_best_values:

This parameter specifies the number of best (least energy) orientations to save in the orientation output file (*.dat) and in the *.e3d partition sum output file (*.e3d). As DOT executes, it saves for each grid point the orientation corresponding to the least energy. The energies at the grid points are then sorted, and some of the least energy values are stored in the output files. The number saved is specified by this option. Specify this parameter as -1 to save all values (this will generate a large output file since SizeX*SizeY*SizeZ will be large).

verbose:

This value indicates at which level DOT should print diagnostic messages to the standard output. These diagnostics include descriptions of what is currently being computed and timing information. Set to '0' for no output to the standard output. Set to '1' for minimal output, and to '2' for modest output on each major step of the calculation.

Autocenter_stl:

This option indicates whether DOT should automatically center the still molecule. The algorithms that DOT uses assume that the still molecule mask is the same as the solvent excluded volume mask used to generate the electrostatic potential grid. In order to satisfy this assumption, the user should set autocenter_stl to "true" only if the centered still molecule was used in the potential calculations. The still molecule can either be centered about (0,0,0) outside of DOT (e.g., using the pdbcenter utility) or by setting the autocenter_stl parameter to "true". It is recommended to use centered still molecules unless there is a specific reason for offsetting the still molecule from the center of the grid.

autocenter_mov:

This option indicates whether DOT should automatically center the moving molecule about (0,0,0) before rotating and translating it throughout the grid by mathematical convolution. It should be always set to "true" for the alpha-release of DOT.

per_orientation_statistics:

Each processor maintains a log file which reports varying levels of statistics. This log file is updated after every rotation performed. It is important to carefully choose a level of reporting which is informative yet that does not store too much data. For large rotation sets, the log files can become large if a high statistical reporting level is requested.

Values for per_orientation_statistics

0	none
1	per orientation best goodness if less than threshold
2	per orientation best goodness
3	per orientation best goodness, electro, and neighborhood if less than threshold
4	per orientation best goodness, electro, and neighborhood
10	per grid cell goodness if above threshold
11	per grid cell goodness

per_orientation_stat_thresh:

Values greater than this threshold will not be reported.

-1000.0

This is the cutoff threshhold for "interesting" energies to be reported in the log files (*.log). This value does not limit the orientations reported in the *.dat and *.e3d files (see saved_best_values).

bumplimit:

In order to accommodate soft docking, the user may specify a tolerance for collisions. The program pdb_to_vol sets the inside of the still molecule to a value of N, where N > the number of atoms in the moving molecule. The program also sets the surface to a negative, attractive value (default –2). Since the moving molecule mask has a value of 1, overlap between the moving molecule and the still molecule will generate a number that is the sum of the product of the number of atoms from the moving molecule that overlap with the surface and the interior of the still molecule. The more atoms that lie in the interior, the larger the number will be. The bumplimit parameter specifies over what value should be considered a hard collision and thus excluded from the results. Increasing the value of the bumplimit allows softer docking.

neighborhood_weight:

This parameter allows the user to set the scaling factor for the steric portion of the run. The energies that DOT reports are a scaled sum between the electrostatic portion of the run and the steric portion of the run. The neighborhood weight parameter scales the steric portion of the run. Setting it to 0 causes all reported energies to be purely electrostatic. Note that DOT still computes the steric portion even if the neighborhood weight is set to 0 so that it can determine which configurations are overlapped and thus not allowed.

do_energy:

This value should be set to true. The parameter is included for future support of free energy calculations.

do_partition_sum:

This value should be set to false. It is included for future support of free energy values.

temperature:

This value is included for future support of free energy calculations and makes no difference in version 1.0_alpha.

sum_type:

This should always be set to "-1" for the alpha-release.

still_grid_clamp_low:

Values in the still molecule mask grid less than this clamp value are set to the low clamp value.

still_grid_clamp_high:

Values in the still molecule mask grid greater than this clamp value are set to the high clamp value.

pot_grid_clamp_low:

Values in the potential grid less than this clamp value are set to the low clamp value.

pot_grid_clamp_high:

Values in the potential grid greater than this clamp value are set to the high clamp value.

SizeX:

The size of the grid in the X dimension. Note that this value is not in Angstroms, but should rather be thought of as the X dimension of an array used to define the grid. The gridstep parameter defines the relationship between grid units and Angstroms.

SizeY:

The size of the grid in the Y dimension. Note that this value is not in Angstroms, but should rather be thought of as the Y dimension of an array used to define the grid. The gridstep parameter defines the relationship between grid units and Angstroms.

SizeZ:

The size of the grid in the Z dimension. Note that this value is not in Angstroms, but should rather be thought of as the Z dimension of an array used to define the grid. The gridstep parameter defines the relationship between grid units and Angstroms. NOTE: DOT algorithms assume that SizeX = SizeY = SizeZ.

gridstep:

The gridstep defines the relationship between adjacent gridpoints and the number of Angstroms spanned. It is assumed that the coordinates for the molecules are in units of Angstroms, so the gridstep is a scaling factor used to place the molecules onto the grid. Setting gridstep to 1 means that each grid point is spaced along the coordinate axes by 1 Angstrom between adjacent gridpoints. NOTE: DOT algorithms assume that gridstep = 1.0 (for the alpha-release).

pot_file:

Specifies the potential file (*.grd) to use to describe the potential field of the still molecule. This should be in Delphi or UHBD format as described elsewhere in this manual.

stl_m_file:

This file specifies the file (*.vol) used to describe the volume of the still molecule. It is the output from pdb_to_vol.

mov_file:

This file (*.dot) specifies the moving molecule atom coordinates and partial charges. It is the output from pdb_to_dot.

rotfile:

This file contains the list of rotations represented as Eulerian angles (theta, phi, psi). DOT will rotate the moving molecule through each of the rotations specified in this list.

outfile:

This parameter specifies the root file name to be used for the log files, the data file, the output file, and the statistics file. Each processor maintains a log file that takes the form of outfile.log0.XYZ where XYZ indicate the processor number. The data file (outfile.dat) contains the best energy (which is a scaled sum of the electrostatic energy and the steric energy), the Cartesian grid coordinates which the best energy occurred at, and the eulerian angles that corresponded to the best energy. The output file (outfile.out) contains DOT stdout.