Output

The output of grid contains several types of information. Like dock, it outputs general information about the current job and echoes the parameters selected from the input file. In addition, it reports information about the receptor and the grids.

Receptor information

Reading in coordinates of receptor.

Merging AMN 163 cap residue with THR1 1 residue.

Merging CXL 164 cap residue with ALA162 162 residue.

CHARGED RESIDUE THR1 : 1.000

CHARGED RESIDUE ARG9 : 1.000

CHARGED RESIDUE LYS51 : 1.000

CHARGED RESIDUE ARG52 : 1.000

CHARGED RESIDUE GLU56 : -1.000

CHARGED RESIDUE ARG57 : 1.000

CHARGED RESIDUE HIP77 : 1.000

CHARGED RESIDUE ASP78 : -1.000

CHARGED RESIDUE LYS127 : 1.000

CHARGED RESIDUE ASP146 : -1.000

CHARGED RESIDUE HIP153 : 1.000

CHARGED RESIDUE GLU156 : -1.000

CHARGED RESIDUE LYS161 : 1.000

CHARGED RESIDUE ALA162 : -1.000

 

Total charge on UNNAMED : 4.000

 

This portion of the output lists any merged cap residues. The cap residues are introduced by sybyl. Charged residues are also listed. If any residues have a non-integer charge, then either the charges were not properly loaded into the receptor input file, or some atoms are missing from the input file. These problems should be resolved before continuing with the grid calculation.

To display more information about parameters that grid assigns to the receptor, use the -v option (see Command-line Arguments on page 79 ).

Grid Information

Reading in grid box information.

Box center of mass : -1.315 36.145 21.153

Box dimensions : 27.525 26.519 26.686

Number of grid points per side [x y z] : 93 90 90

Total number of grid points : 753300

 

Generating scoring grids.

Percent of protein atoms processed : 0

Percent of protein atoms processed : 10

Percent of protein atoms processed : 20

...etc...

 

Information about the grid geometry is reported. The total number of grid points can be adjusted by changing the input box dimensions or changing the grid spacing. Generally a value under 1 million is appropriate, but this depends on system resources.

The progress of the calculation is reported as the percent of protein atoms processed. This calculation usually takes up to 30 minutes depending on the grid geometry and the receptor size.

 

UC Regents 1998
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