Minimize Structure

Minimize Structure energy-minimizes molecule models, optionally holding some atoms fixed. The Amber 1994 force field is used for standard residues, and Amber's Antechamber module (included with Chimera) is used to assign parameters to nonstandard residues. Minimization routines are provided by MMTK, also included with Chimera.

Minimize Structure is in an early phase of development and has several limitations.

There are several ways to start Minimize Structure, a tool in the Structure Editing category. It is also implemented as the command minimize.

Models to minimize can be chosen from the list with the left mouse button. Ctrl-click toggles the status of an individual model. To choose a block of models without dragging, click on the first (or last) and then Shift-click on the last (or first) in the desired block. All chosen models are treated as a single system for energy calculations.

Minimization parameters:

• Steps (default 100) - the total number of minimization steps to perform
• Update interval (default 10) - how frequently to update the display, in terms of minimization steps
• Fixed atoms - atoms to hold in place during minimization:
  • none (default) - all atoms will be allowed to move
  • selected - any selected atoms should be held fixed, all other atoms allowed to move
  • unselected - any selected atoms should be allowed to move, all other atoms held fixed

Before energy calculations can be performed, it is necessary to correct structural inconsistencies, add hydrogens, and associate atoms with force field parameters. Clicking Minimize dismisses the dialog (unless the option to Keep dialog up after Minimize is checked) and may call Dock Prep to perform several tasks to prepare the structure(s). Dock Prep may in turn call other tools (AddH and Add Charge). The tasks are checkbox options that can be turned on or off independently, allowing control over whether adjustments such as deleting solvent will be applied, or skipping of any steps that have already been performed. For example, hydrogens might have been added before the Minimize button was clicked, so that they could be selected and designated as the atoms allowed to move during minimization.

Currently, Add Charge (or the command addcharge) must be used on a structure prior to minimization because it plays a crucial role in assigning parameters. Users can, however, specify alternative charges for nonstandard residues.

Close dismisses the Minimize Structure dialog, and Help opens this manual page in a browser window.

Force Field Parameters

Different procedures are used to assign parameters to atoms in standard and nonstandard residues.

Standard residues include water, standard amino acids, standard nucleic acids, and a few common variants and capping groups.

1. Add Charge recognizes standard residues based on their atom and residue names and assigns Amber residue names. This is done with the attribute assignment file named amberName.defattr in the share/AddCharge/ directory of a Chimera installation.
   
   
2. Minimize Structure uses the Amber residue names to associate standard residues with parameters (including charges) from the Amber 1994 force field:

   W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, Jr., D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, and P.A. Kollman, "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules" J Am Chem Soc 117:5179 (1995).

   Water charges correspond to the TIP3P model:

   W.L. Jorgensen, J. Chandrasekhar, and J.D. Madura, "Comparison of simple potential functions for simulating liquid water" J Chem Phys 79:926 (1983).

Nonstandard residues are all residues not recognized as standard.

1. For nonstandard residues, Add Charge uses Amber's Antechamber module (included with Chimera) to assign gaff types and calculate partial charges. It is necessary to specify the formal charge of each nonstandard residue and which charge calculation method should be used.

   Publications involving Antechamber use should cite:

   J. Wang, W. Wang, P.A. Kollman, and D.A. Case, "Automatic atom type and bond type perception in molecular mechanical calculations" J Mol Graph Model 25:247 (2006).

2. Minimize Structure uses the gaff types to associate nonstandard residues with parameters other than charges. The gaff atom types and associated parameters are described in:

   J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman, and D.A. Case, "Development and testing of a general amber force field." J Comput Chem 25(9):1157 (2004).

User-Specified Charges

For nonstandard residues only, it is possible to use charges other than those assigned by Add Charge. To do so,

1. run Dock Prep independent of Minimize Structure to perform any necessary tasks plus charge addition (thus running Add Charge)
2. reassign the charge attribute of the atoms to the desired values (for example, using Define Attribute)
3. run Minimize Structure and turn off all options in the ensuing Dock Prep dialog, as the necessary tasks have already been performed

This procedure does not allow alternative charges to be used for atoms in standard residues, because Minimize Structure will always associate those atoms with the standard parameters, including charges.

Limitations

Lack of access to many settings. There is no way to specify MMTK minimization settings (other than the number of steps), force field options such as interaction cutoff distances, or the use of restraints. The MMTK default settings are used.

No choice of force field. The only choice in MMTK suitable for biomolecular simulations is Amber 94. The gaff parameters are used for nonstandard residues because they are consistent with Amber standard residue parameters, and because Antechamber can provide the necessary gaff type assignments.

Limited ability to use arbitrary parameters. For nonstandard residues only, users can specify arbitrary partial charges, but the process is somewhat involved.

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UCSF Computer Graphics Laboratory / September 2006