The ENERGY commands specify parameters for energy calculations and can calculate potential energy (including force gradients) of SELECTED ATOMS (or POINTs). Within ENERGY command the individual ENERGY terms are turned "ON" and "OFF", "CUTOFF" distance for ELECTROSTATIC and van der Waals (VDW) energy terms and "SCALE" is specified. You can inspect these parameters with
> show energy
command. Detailed information about geometry and possible threshold violations of each particular energy term can be inspected using "LIST" and "RANGE" keywords.
"FORCES" can be inspected with
> show forces select ... end > image sele ... end force real.
DEFINE commands enable ENERGY calculations, so check there first when facing any unexpected behavior.
Related commands are "DEFINE" (define.html, MAIN_UTILS:def_top_par_19.com) "MINIMIZE (minimize.html, MAIN_CMDS:refine.cmds", and"ANALYZE"("anal.txt", MAIN_MENU:analysis.txt")
> ENERGY
ALL ON / OFF
ANGLE ON / OFF
SCALE
B-VALUES ON / OFF
SCALE real
BOND real
ANGLE real
GROUP real
MINIMAL real
MAXIMAL real
OVERALL
INDIVIDUAL
BOND ON / OFF
SCALE
CON_DIHE ON / OFF
SCALE
CUTOFF real
DENSITY ON / OFF
MAP intg
SCALE / RATIO real
GRID intg
ATOM
POINTS
POLYNOMI
CONVOLUT
DIELECTRIC real
DIHEDRAL ON / OFF
SCALE
ELECTROS ON / OFF
EXCLUDE intg
HBOND ON / OFF
SCALE
IMPROPER ON / OFF
SCALE
LIST
MATRIX
NCS ON / OFF
SCALE real
PAIR ON / OFF
SCALE real
RANGE real real
SELECT ... END
TRANSLATE VECTOR real real real
ATOM iatom
POINT intg
VDW ON / OFF
SCALE real
X-TARGET ON / OFF
SCALE
... ALL ON
OFF
Turns ALL energy terms OFF. The ON command, however, turns on only the default terms (BOND, ANGLE, DIHEDRAL, IMPROPER, ELECTROSTATICS, VDW).
> energy all off
... ANGLE ON
OFF
SCALE real
The ANGLE energy controls the ideality of a A-B-C angle, using rotation derivatives for A-B and C-D bonds in the A-B-C plane.
The ON and OFF commands control the status of the ANGLE term, wherase the SCALE allows you to additionally control the strength of the term by scaling it up (real> 1) or down (real< 1). The default scale is 1.0.
... B-VALUES ON / OFF
SCALE real
BOND real
ANGLE real
GROUP real
MINIMAL real
MAXIMAL real
OVERALL
INDIVIDUAL
B-VALUE energy is actually a group of energy terms, which all together constitute the B-VALUE energy that can be optimized using
> minimize b-value
commands. The B-VALUE is a term by itself too. It is the pulling force of the atomic B-factors, whereas the BOND, ANGLE, GROUP, MINIMAL and MAXIMAL impose soft or hard con- and re-straints on atomic B-values.
> show temp ... > anal temp ...
commands give you some insight into the B-values distributions. See also "ANAL_TEM" in MAIN_MENU:analysis.html.
See also related documantation on B-value refinement in MAIN_DOC:refine/refine.html, on menu item "REFINE_B in MAIN_MENU:map_atom.html and the MAIN_CMDS:refine_b.cmds macro.
... SCALE real
SCALES the atomic B-factor against the underlaying density map. In the case of X-TARGET optimization, this scale has no effect (to be implemented yet).
> energy b-valu scale = 100.0
... BOND real
Restraints B-values of two covalently bound groups by a specified harmonic force constant.
... ANGLE real
Restraints B-values of two groups covalently attached to the same atom by a specified harmonic force constant.
... GROUP real
Restraints B-values of aall atoms being a member of a DEFINED group (define.html) to the arithmetic middle of the group by a specified harmonic force constant. If the constant is a negative number then the restraint is hard and the shifts in atomic B-values during mininmization are averaged.
Each group can be of any size, the smallest group is individual atom.
... MINIMAL real
Specifies the lowest B-value limit. MAIN does not except values lower than 2.0. Constraints atomic B-values to the values above the specified MINIMAL border.
... MAXIMAL real
Specifies the highest B-value limit. Constraints atomic B-values to the values below the specified MAXIMAL border.
... BOND ON
OFF
SCALE real
The BOND energy controls the ideality of a A-B distance using harmonic constraints.
The ON and OFF commands control the status of the BOND term, wherase the SCALE allows you to additionally control the strength of the term by scaling it up (real> 1) or down (real< 1). The default scale is 1.0.
... CON_DIHE ON / OFF
SCALE
Controls the dihedral constraints as specified by "DEFINE CONSTRAINTS DIHEDRAL" command (MAIN_COM:define.html).
The ON and OFF commands control the status of the CON_DIHE term, wherase the SCALE allows you to additionally control the strength of the term by scaling it up (real> 1) or down (real< 1). The default scale is 1.0.
... CUTOFF real
Defines CUTOFF distance for the nonbonding energy terms. Default value is 8 A.
... DENSITY ON / OFF
SCALE real
MAP intg
GRID intg
ATOMS
POINTS
POLYNOMI
CONVOLUT
DENSITY energy is kind of correlation between placement of a group of ATOMS or POINTS with a density MAP. The term has a SCALE.
... DENSITY ATOMS ...
Calculates energy and derivatives for ATOMS instead of points. Uses POLYNOMIAL or CONVOLUTION terms. POLYNOMIAL is the default.
... POLYNOMIAL
Each atom density ENERGY contribution is calculated from three second order polynomials approximation. The coeficients for the second order polynomials are calculated by a least square fit procedure from four density points. The points are laying on the line parallel to an crystall cell axis passing through an atomic center position on grid layers (1, 0, +1, +2), whereas the atomic center defines the 0 grid layer. It is positioned between the 0 and +1 grid layer.
The density values of the four density points are obtained by a linear interpolation from their four neighbor grid points which lay in the layer perpendicular to the line direction.
From these polynomials an atomic density energy is calculated as negative of the averaged summ of all three directions contributions scaled by the DENSITY SCALING factor. Derivatives are calculated along each cell axis direction on the basis from each polynomial approximation.
... CONVOLUTION
Calculates energy as the the convolution of underaying electron density map with atomic electron density generated from atomic scattering factors taking into account their B-values. Derivatives are calculated numerically by shifting atom centers in X, Y and Z directions.
Although this seems to be the best possible way top calculate the density correlation, you are advised to use it with caution since it is a computer time consuming method.
... DENSITY POINTS
In the case of POINTS DENSITY the energy is a product of the interpolated density at the point positions and the value of each particular point. Combined together with SET CENTER, SET MATRIX and TRANSLATE options, it can be used for optimizing local symmetry, Patterson map superposition by rotational searches, and cross peak correlations of a difference Patterson map. The use of loops is recommended.
> energy all off density on density points density scale 1.0 > set matrix 2 polar 45. 78. 180. > set center coordinates 40. 41. 67. > energy matrix 2 translate vector 20. 20. 34. select all end
The DENSITY energy of a POINT selection is the interpolated density from a map to the center position. (The DENSITY energy term is so essentailly a correlation.) The density values are interpolated from the closest GRID intg specified number of grid layers around each selected point position in box (2*2*2=0, 4*4*4=1, 6*6*6=3, 8*8*8=4).
... GRID inte
Works in combination with the POINTS correlation term.
... DIELECTRIC real
Defines the dielectric constant for electrostatic calculations. Default value is 1.
... ELECTROSTAT ON / OFF
Electrostatic calculations are based on interactions of partial atomic charges interacting via Coulombe law.
The command turns ON and OFF the electrostatic term. Its scale is defined vie DIELECTRIC constant.
... EXCLUDE intg
The EXCLUDE command defines the level of neighboring atoms to the current atom in nonbonding energy (VdW and ELECTROSTATIC) calculations. The level is defined by integer. For example: CA is bound to N, CB and C. Level 1 means that the nonbonding interactions between atom CA and N, CB or C will be scaled with a scaling factor for electrostatics. No atom will be excluded from nonbonding interactions. The interactions with other atoms are not scaled.
Level 2 means that atoms N, CB and C will be excluded from nonbonding interactions, but that the interactions between their neighbors (HN, -C, CG, O, +N ) and CA will be scaled with the scaling factor. And so on.
The default level for X-PLOR force fields is 3 and scaling constant is 0.4 for the border atoms interaction (electrostatic scale).
However, level -1 means, that atoms comprising a molecule are interacting only with atoms from the other molecules. (A molecule consist of atoms linked into a covalent bonds network.)
... HBONDS ON / OFF
SCALE
The HBOND energy controls the ideality of hydrogen bond donnor and acceptor distance using week harmonic constraints.
The ON and OFF commands control the status of the BOND term, wherase the SCALE allows you to additionally control the strength of the term by scaling it up (real> 1) or down (real< 1). The default scale is 1.0.
... IMPROPER ON / OFF
SCALE
The IMPROPER energy controls the ideality of a A-B-C-D dihedral angle using periodic or harmonic constraints to enforce the planarity or chiralty of the atoms.
The ON and OFF commands control the status of the BOND term, wherase the SCALE allows you to additionally control the strength of the term by scaling it up (real> 1) or down (real< 1). The default scale is 1.0.
The LIST RANGE real real sets the list flag. The meaning is that all interatomic interactions of all energy terms turned on will be written to the terminal. RANGE sets the threshold values. If no real number is specified, the threshold value is set to 0.0. The first real number relates to geometry violations, and the second one to the energy of interaction. Range command has no effect when the LIST flag is not set.
For bonding terms: BOND, ANGLE, DIHEDRAL, IMPROPER
If range is active then only the terms that have a deviation from the ideal value greater than that specified or an energy term larger than specified, will be printed.
For nonbonding terms: ELECTROSTATIC, VdW
If range is active only the pair of atoms with their absolute energies above the specified threshold will be printed.
Useful for debuging purposes mostly.
... MATRIX inte
Specifies the rotation MATRIX (1-8) which will be applied in point rotations used in calculations of electron density maps correllations.
... NCS ON / OFF
SCALE real
The NCS (Non-Crystallographic-Symmtry) constraints pull the DEFINED groups against their arithmetic middle position with a group force. Here you can specify also additional overall SCALE value.
... PAIR ON / OFF
SCALE real
The PAIR energy controls the distance of a atoms on the PAIR list using harmonic constraints. The target distance value and force are DEFINED for each particular pair on the list.
The PAIR terms enable you to enforce certain interatomic distances (MAK_PAIR).or softly constrain atoms to a certain positions (ANCHORS).
The ON and OFF commands control the status of the BOND term, wherase the SCALE allows you to additionally control the strength of the term by scaling it up (real> 1) or down (real< 1). The default scale is 1.0.
... RANGE real real
Specifies the RANGE (threshold) values above which each interatomic interaction exceeding the threshold will be listed. The first real relates to geometry terms (BOND, ANGLE, DIHEDRAL and IMPROPER), whereas the second relates to to the ENERGY of each particular interactions. The command
> energy all off bond on list sele resi numb 1 end range 0.3
Lists all bonds that deviate for more than 0.3 A from the target value.
... SELECT ... END (SELECT ... END)
Two SELECTIONS can be specified. The first selection defines atoms on which forces are calculated, the second selection defines the atoms on which the first atom selection interacts. In order to calculate the potential energy of a molecule, its atoms should be defined in both selections.
When only one SELECTION is defined it is assumed that the second selection is equal to the first one. When no SELECTION is specified no ENERGY calculation is perfomed.
... TRANSLATE VECTOR real real real
ATOM inte
POINT inte
Specifies the TRANSLATION which will be applied to POINT rotations and translations used in calculations of electron density maps correllations.
The translation vector can be specified explicitely or via an ATOM or POINT position. When ATOMs or POINTs or points are applied and the underlaying map is a Patterson map, then the procedure corresponds to a cross-vector verification.
... VDW ON / OFF
SCALE real
The VDW energy controls interatomic distances repulsive and attractive Van der Waals distance dependent terms.
The ON and OFF commands control the status of the BOND term, wherase the SCALE allows you to additionally control the strength of the term by scaling it up (real> 1) or down (real< 1). The default scale is 1.0.
... X-TARGET ON / OFF
SCALE real
Turns ON or OFF the (Fo-Fc)**2 target used in crystallographic refinement. The X-TARGET ON command turns the DENSITY term off.
The X-TARGET uses the currently valied DENSITY MAP for FFT transformation, so be sure that that map is a complete unit cell.