Minimize is the command-line implementation of Minimize Structure; it energy-minimizes molecule models, optionally holding some atoms fixed. 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.
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.
spec atom-spec
Whether to restrict minimization to a subset of the open molecule models. The entire model(s) containing the specified atoms will be considered. If atom-spec includes any spaces, it must be enclosed in single or double quote marks. All specified models are treated as a single system for energy calculations.
nsteps N
N (default 100) is the maximum number of minimization steps to perform.
stepsize D
D (default 0.02 Å) is the initial step length.
interval M
M (default 10) is how often to update the display, in terms of minimization steps.
freeze none|selected|unselected
In the specified models, which atoms to hold in place during minimization: none (default), the currently selected atoms, or all atoms that are not selected.
nogui true|falseSee also: addh, addcharge, findclash, Dock Prep, Adjust Torsions, Minimize Structure
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 ff99 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). Synonyms for true: True, 1. Synonyms for false: False, 0.