Minimize Structure

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

Minimize Structure is in development and has several limitations. It is intended for cleaning up small molecule structures and improving localized interactions within larger systems. It may not be able to resolve large-scale distortions or widespread structural problems. By definition, energy-minimization simply moves the system toward a local minimimum without crossing energy barriers, and does not search for the global minimum.

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. Within the chosen models, all atoms are included in energy calculations, regardless of whether they are held fixed. (However, parts of models can be excluded from energy calculations using the minimize command with fragment true.)

Steepest descent minimization is performed first to relieve highly unfavorable clashes, followed by conjugate gradient minimization, which is much slower but more effective at reaching an energy minimum after severe clashes have been relieved. Energies (kJ/mol) are reported in the Reply Log. **Step numbers reported by MMTK are 2 greater than the actual numbers of minimization steps performed. The additional “steps” are not minimization steps but operations required to obtain gradient values and updated coordinates.**

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: It is sometimes useful to run Dock Prep independent of Minimize Structure beforehand, then skip all tasks when it reappears after Minimize is clicked: 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, Amber atom types, and atomic partial charges from an Amber force field chosen by the user, default ff14SB (details).
  2. Minimize Structure uses the Amber atom types to associate the atoms with other parameters from the chosen force field.
Monatomic ions are assigned user-specified net charges and Amber VDW parameters. The following ions are handled: Li+, Na+, K+, Rb+, Cs+, F, Cl, Br, I, Mg2+, Ca2+, Zn2+. In addition, Fe ion nonbonded parameters are taken from the heme residue in the Amber parameter database. See Limitations for how to add types.

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

  1. Add Charge uses Amber's Antechamber module (included with Chimera) to assign GAFF types and calculate atomic partial charges within each nonstandard residue. 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:
    Automatic atom type and bond type perception in molecular mechanical calculations. Wang J, Wang W, Kollman PA, Case DA. J Mol Graph Model. 2006 Oct;25(2):247-60.
    Note that Antechamber/GAFF are meant to handle most small organic molecules, but not metal complexes, inorganic compounds, or unstable species such as radicals, and may not work well on highly charged molecules.

  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 online and in:
    Development and testing of a general amber force field. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. J Comput Chem. 2004 Jul 15;25(9):1157-74.

User-Specified Partial Charges

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, which is still needed to assign Amber/GAFF atom types)
  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


Lack of access to many settings. There is no way to specify several MMTK settings, including distance cutoffs. MMTK defaults are used. Evaluating all pairwise nonbonded interactions regardless of interatomic distance makes the calculation relatively slow.

Limited ability to use arbitrary parameters. It is difficult to change or add parameters. Arbitrary partial charges can be specified. Experts can adjust parameters (other than charge) of standard residues and monatomic ions by editing files in bin/amber14/dat/leap/parm/ within the Chimera installation. The following parameter files are used:

In addition, a custom frcmod file (not included with the Amber distribution) is used to specify Fe ion nonbonded parameters taken from the heme residue in the Amber parameter database (Bryce Group, University of Manchester).

To add an element that is not already handled, it may also be necessary to create a file for that element in the MMTK atom database within the Chimera installation. For example, to handle Li+, there is a file lib/python*/site-packages/MMTK/Database/Atoms/li (where * is the appropriate python version number) containing the following:

name = 'lithium'
symbol = 'Li'
mass = 6.941

UCSF Computer Graphics Laboratory / September 2015