Usage:
minimize  options

Minimize is the command-line implementation of Minimize Structure; it 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 (included with Chimera) is used to assign parameters to nonstandard residues.

Before energy calculations can be performed, it is necessary to correct structural inconsistencies, add hydrogens, and associate atoms with force field parameters. Minimize calls Dock Prep to perform several tasks to to prepare the structure(s). Dock Prep may in turn call other tools (AddH and Add Charge). Currently, Add Charge (or the command addcharge) must be run prior to minimization because it plays a crucial role in assigning parameters.

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.**

Please consult the Minimize Structure manual page for further details.

Option keywords for minimize can be truncated to unique strings and their case does not matter. A vertical bar "|" designates mutually exclusive options, and default values are indicated with bold. Synonyms for true: True, 1. Synonyms for false: False, 0.

spec atom-spec
Minimize/move only the atoms in atom-spec. All other atoms will be held in place automatically, without explicit use of freeze. However, energy calculations will include the entire molecule models containing the specified atoms, unless fragment true is also used. All included models are treated as a single system. If atom-spec contains any spaces, it must be enclosed in single or double quote marks.

fragment  true | false
Instead of the entire models, include in energy calculations only the residues containing the spec atoms. Residues can only be included/excluded as a whole, and all included residues (even if from multiple models) are treated as a single system. Note, however, that any subset of the spec atoms can be frozen in place.

cache  true | false
Whether to cache parameters such as partial charges for the current system (models or fragment to be included in energy calculations). Caching allows reusing the data in subsequent rounds of minimization after simply updating the coordinates. Cached data for a system will be kept indefinitely unless Chimera detects a change in that system (atom addition or deletion); setting cache false helps to prevent overconsumption of memory.

prep  true | false
Whether to call Dock Prep when parameters for the current system are not in the cache. (If the parameters for the system are in the cache, Dock Prep will not be called, regardless of this setting.) The purpose of prep false is to avoid re-preparing structures that have already been prepared but not cached (for example, a different fragment than was previously minimized).

freeze  none | selected | unselected | atom-spec
Which atoms (in addition to those frozen automatically) to hold in place during minimization: none (default), those which are selected, those which are not selected, or those indicated with an atom-spec. Previously this option was required to freeze any atoms, but now that atoms other than the spec atoms are frozen automatically, this option is only needed in the case of:

1. restricting the calculation to certain residues with the spec option and fragment true
2. additionally freezing some of the spec atoms

This combination of options is useful for preventing long or distorted bonds at the junction between included and excluded residues. For example, minimizing a linker between two domains that are excluded from the calculation could significantly degrade the linker-domain bonds (since those bonds are ignored) unless the linker endpoint atoms are frozen in addition to the domains.

nsteps N
N (default 100) is the number of steps of steepest descent minimization to perform before any conjugate gradient minimization.

stepsize S
S (default 0.02 Å) is the initial step length for steepest descent minimization.

cgsteps M
M (default 10) is the number of steps of conjugate gradient minimization to perform after finishing any steepest descent minimization.

cgstepsize D
D (default 0.02 Å) is the initial step length for conjugate gradient minimization.

interval I
I (default 10) is how often to update the display, in terms of minimization steps.

nogui  true | false
Setting nogui to true suppresses the appearance of tool dialogs that might otherwise appear. Dock Prep and AddH are executed with their default settings (as shown when running minimize with nogui false), while Add Charge uses Amber ff14SB charges for standard residues (details) and for any nonstandard residues, the method last specified in its GUI (AM1-BCC if the GUI has not been used).