MacroModel Coordinate Scan

Options

Output Column Structure

Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaced within Input columns - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Include Log in output

Include the Macromodel log in the output data table

Force Field

Available force fields: MM2, MM3, AMBER, OPLS, AMBER94, MMFF, MMFFs, OPLS_2005 (default)

Solvent

Available Solvents: None (i.e. vacuum), Water

Minimization Algorithm

PRCG, TNCG, OSVM, SD, FMNR, LBFGS, TNCG, Optimal

Electrostatic treatment

Force field defined (default), distance dependent, constant dielectric

Dielectric constant

defaults to 1.0

Minimization steps

Maximum number of minimization steps

First coordinate to scan

The first coordinate to scan entered as 2 (distance), 3 (angle) or 4 (dihedral) integers separated by a comma, space or tab.

Column containing first coordinate to scan

Column in input table containing the first coordinate to scan with format as above.

Initial

Specify the initial value for the first coordinate. The default value to enter is 1.0 angstroms for distances and 0.0 degrees for angles and dihedrals.

Final

Specify the final value for the first coordinate. The default value to enter is 10.0 angstroms for distances and 360.0 degrees for angles and dihedrals.

Coordinate type

Select the coordinate type: Distance (two integers), Angle (three integers) and Dihedral (four integers).

Increment

Specify the increment for the first coordinate. An increment can be negative only if the initial value is larger than the final value. The default value to enter is 1.0 angstroms for distance. The minimum angle or dihedral increment is 1 degree, but scans with such fine resolution usually provide less useful information than those with a resolution of 10 degrees. The former also takes more time. The default value to enter for angle or dihedral is 30 degrees.

Use second coordinate for scan

Allows setting of a second coordinate to be scanned, however this must be of the same type as the first i.e. distance, angle or dihedral.

Second coordinate to scan

The second coordinate to scan entered as 2 (distance), 3 (angle) or 4 (dihedral) integers separated by a comma, space or tab.

Column containing second coordinate to scan

Column in input table containing the second coordinate to scan with format as above.

Initial

Specify the initial value for the second coordinate. The default value to enter is 1.0 angstroms for distances and 0.0 degrees for angles and dihedrals.

Final

Specify the final value for the second coordinate. The default value to enter is 10.0 angstroms for distances and 360.0 degrees for angles and dihedrals.

Increment

Specify the increment for the second coordinate. An increment can be negative only if the initial value is larger than the final value. The default value to enter is 1.0 angstroms for distance. The minimum angle or dihedral increment is 1 degree, but scans with such fine resolution usually provide less useful information than those with a resolution of 10 degrees. The former also takes more time. The default value to enter for angle or dihedral is 30 degrees.

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