Minimize Structure

Minimize Structure energy-minimizes molecule models, optionally holding some atoms fixed. Minimization routines are provided by MMTK, which is included with Chimera. The Amber ff99 force field is used for standard residues, and Amber's Antechamber module (also included with Chimera) is used to assign parameters to nonstandard residues.

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; other models are ignored.

Currently, only steepest descent minimization is performed.

• Steps (default 100) - maximum number of minimization steps
• Step size (A) (default 0.02 Å) - initial step length
• 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

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 system for energy calculations. In turn, Dock Prep may call additional tools:

• AddH to add hydrogens. If Minimize has already been clicked, the selection will be adjusted prior to minimization to include any newly attached atoms in the fixed and movable sets. Note that any other models in the vicinity will influence hydrogen placement even if hydrogens are not being added to those other models. If such interactions are not desired, the other models should be closed beforehand.
  
  
• Add Charge to associate atoms with partial charges and other force field parameters. Required even when alternative charges will be used.

It is sometimes useful to run Dock Prep independent of Minimize Structure beforehand, then skip all tasks when it reappears after Minimize is clicked:

• adding hydrogens separately beforehand allows them to be deleted or repositioned as needed prior to minimization
• adding charges separately beforehand allows alternative charges to be specified prior to minimization

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

Force Field Parameters

Different procedures are used to assign parameters to standard residues, monatomic ions, 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 Amber ff99 parameters. Many parameters (including the partial charges) are the same as described in:

   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).

Monatomic ions are assigned user-specified net charges and Amber ff99 VDW parameters. Only the ions in ff99 are handled: Na⁺, K⁺, Rb⁺, Cs⁺, Mg²⁺, Ca²⁺, Zn²⁺, and Cl^–.

Nonstandard residues are all residues not recognized as standard residues or monatomic ions.

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 Partial Charges

For nonstandard residues, arbitrary partial charges (such as obtained from the literature or parameter databases) can be specified. To do so:

1. run Dock Prep independent of Minimize Structure to perform any necessary tasks including charge addition (thus running Add Charge)
2. reassign the charge attribute of the atoms to the desired values (using Define Attribute, defattr, or setattr)
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 will not work 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 certain MMTK minimization settings, force field options, or restraints. The MMTK defaults are used.

No choice of force field. The only force field in MMTK suitable for biomolecular simulations is Amber. 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. It is difficult to change or add parameters. For nonstandard residues only, arbitrary partial charges can be specified. Other changes require manually editing parameter files within the Chimera installation:

• partial charges in standard residues: share/AddCharge/charge.defattr (it is necessary to run attr2dict.py in that same directory after making any changes; see details)
• other parameters of standard residues and monatomic ions: lib/python*/site-packages/MMTK/ForceFields/amber/amber_parm99, where * is a python version number

---

UCSF Computer Graphics Laboratory / May 2008