Minimize as Rigid Body - Constraints Dialog Box
In this dialog box, you can set up constraints on distances and restraints of atoms to initial positions when performing rigid-body minimizations.
To open this dialog box, click Constraints in the Minimize as Rigid Body panel.
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Using the Minimize as Rigid Body - Constraints Dialog Box
Distance constraints can be useful when minimizing a structure as rigid bodies. For example, you could use them to pull a ligand into the desired position while keeping it rigid, and to force open and closed a large "clam-shell" protein, while keeping each half of the "shell" internally rigid.
Cartesian constraints can be useful for preventing a rigid body that's being minimized from drifting too far.
Minimize as Rigid Body - Constraints Dialog Box Features
Distance tab
In this tab you can constrain the distance between pairs of atoms. Normally, these constraints are made between nonbonded atoms, but you can pick bonded atoms as well. The constraintsare applied as harmonic constraints. These constraints set PAIR_CONSTRAINT_i keywords in the input file.
- Define atoms for distance constraint picking tools
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Use these picking tools to pick pairs of atoms for which a distance constraint will be applied. When you pick the second atom, a row is added to the constraints table, with the atom-atom distance and a default force constant for the constraint.
- Constraints table
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This table lists the constraints. It has four columns, which are described below. You can select a single row in the table.
Atom1 Index of first atom in constraint. Noneditable. Atom2 Index of second atom in constraint. Noneditable. Distance Distance to which atoms are constrained. The initial value is the distance between the atoms in the Workspace structure. You can change the distance by editing the table cell. Force Constant Coefficient of the harmonic constraint potential (actually half the force constant), in kcal mol-1 Å-2. You can change the value by editing the table cell. The default is 350; if you clear the table cell it is reset to 350. - Delete and Delete All buttons
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Delete the constraint that is selected in the table by clicking Delete; delete all constraints by clicking Delete All.
Cartesian tab
In this tab you can restrain atoms to within a given distance of their initial coordinates with a flat-bottomed potential.
- Restrain atoms to their initial coordinates picking tools
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Use these picking tools to pick atoms for which a flat-bottomed harmonic restraint will be applied.
- Force constant text box
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Coefficient of the harmonic constraint potential (actually half the force constant), in kcal mol-1 Å-2. The default is 10.
- Distance text box
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Radius of the flat-bottomed part of the restraining potential. This is the distance that an atom can move freely from its initial position before it experiences the restraining potential.