Minimize Structure energy-minimizes molecule models, optionally
holding some atoms fixed. Minimization routines are provided by
which is included with Chimera. The
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
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.
steepest descent minimization is performed.
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:
- 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
should be held fixed, all other atoms allowed to move
- unselected - any
should be allowed to move, all other atoms held fixed
It is sometimes useful to run
Dock Prep independent of
Minimize Structure beforehand, then skip all tasks when it reappears
after Minimize is clicked:
- AddH to add hydrogens.
If Minimize has already been clicked,
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.
Close dismisses the Minimize Structure dialog.
Help opens this manual page in a browser window.
- adding hydrogens separately beforehand allows them
to be deleted or repositioned as needed prior to minimization
- adding charges separately beforehand allows
to be specified prior to minimization
Force Field Parameters
Different procedures are used to assign parameters to
monatomic ions, and
Standard residues include water, standard amino acids,
standard nucleic acids, and a few common variants and capping groups.
Monatomic ions are assigned user-specified net charges and
ff99 VDW parameters. Only the ions in ff99 are handled:
Na+, K+, Rb+, Cs+,
Mg2+, Ca2+, Zn2+,
- Add Charge
recognizes standard residues based on their atom and residue names
and assigns Amber residue names. This is done with the
assignment file named amberName.defattr in the
share/AddCharge/ directory of a Chimera installation.
- Minimize Structure uses the Amber residue names to associate
standard residues with
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).
Nonstandard residues are all residues not recognized as
standard residues or
- 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.
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).
- 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:
This procedure will not work for atoms in
standard residues, because
Minimize Structure will always associate those atoms
with the standard parameters, including charges.
- run Dock Prep independent
of Minimize Structure to perform any necessary tasks
including charge addition (thus running
- reassign the charge attribute of the atoms
to the desired values (using
- 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 certain MMTK
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
The gaff parameters are used for
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
- other parameters of standard residues
and monatomic ions:
where * is a python version number
UCSF Computer Graphics Laboratory / May 2008