17.1.3.3 Static Properties of Atoms

The following table describes the syntax and function of the various properties available for atoms.

Syntax

Function

`X'

X coordinate of atom.

`Y'

Y coordinate of atom.

`Z'

Z coordinate of atom.

`R'

Distance of atom from geometric center. When this property is computed for a difference table, it returns the length of the vector between the two atoms being compared. If either atom in the pair has an undefined position, then the distance will be calculated as zero.

`NUMBER'

Sequence number of atom.

`ENERGY, FORCE'

The total potential energy (or force) per atom. This is calculated as follows: we start with the non-bonded energy per atom. The energy of each bond is split evenly among the two atoms. The bond angle energy is summed onto the central atom. The torsion angle energy is split between the center two atoms. The improper torsion energy is summed to the center atom. The harmonic constraint energy is is added to every atom. Finally, the hydrogen bond energy is split between the donor and acceptor atom. FORCE is magnitude of the force vector at each atom (sqrt((dE/dx)^2 + (dE/dy)^2 + (dE/dz)^2)). The individual force terms are summed prior to calculating the magnitude.

`EB, FB'

Bond energy (or force) per atom - the energy of each bond split evenly among two atoms is summed for each each atom.

`ET, FT'

Angle energy (or force) per atom - The sum of the energies of all angles whose central atom is the atom.

`EP, FP'

Torsion angle energy (or force) per atom - The energy of each torsion angle is split among the two central atoms and summed over all the atoms.

`EI, FI'

Improper torsion angle energy (or force) per atom. The energy of all improper torsions is summed onto the center atom.

`EHB, FHB'

Hydrogen bond energy (or force) per atom - The energy of each hydrogen bond is split across each atom in the pair.

`EVDW, FVDW'

Van der Waals energy (or force) per atom - calculated the same way as ELEC.

`ELEC, FELE'

Electrostatic energy (or force) per atom - this is calculated by taking the pairwise electrostatic energy for each non-bonded pair and summing half of this energy on each atom in the pair.

`ELED, FELD'

Direct part of the electrostatic interaction. This is the same as ELEC if reaction fields are not being calculated.

`ERXN, FRXN'

The reaction field energy (or force). WARNING: the reaction field calculation was under development in CHARMM v.16. Please review the code before attempting any calculations with this option.

`ENB, FNB'

Non-bonded energy (or force) per atom - sum of EVDW and ELEC.

`EC, FC'

Harmonic constraint energy, or force.

`EUSER, FUSER'

The energy (or force) returned by the USERE subroutine. See CONGEN Modifications, for a description of USERE which provides more information on writing user energy routines. Note that the USERE routine must be written to return the appropriate data for analysis of energies (versions of USERE routines which do not support the analysis of energies will run in the main part of the program even though they will bomb out if called from analysis).

`EPBE'

The electrostatic energy of each atom as calculated by the Poisson-Boltzmann equation. This calculation is done by creating an empty charge density array, looping through each atom in the system, charging the array specifically for each atom, and calculating the electrostatic energy, see PBE ENERGY Command.

`EPSPBE'

The actual dielectric constant for each atom as used by the Poisson-Boltzmann equation. This property is useful for checking the effects of adjusting dielectric constants based on exposed surfaces, see PBE SETUP Command.

`SURFACE'

The accessible surface of the atom in square Angstroms as calculated by Lee and Richard's accessible surface program. A probe diameter of 1.4 A is used with a fractional error parameter of 0.05. These two parameters can be changed using the analysis set command, see Analysis Set Command. This surface includes the radius of the probe.

`CONTACT'

The contact area as calculated by Lee and Richard's accessible surface program¹. The contact area does not include the radius of the probe. The parameters are the same as in the SURFACE property.

`RADIUS'

The Van Der Waals radius of the atom as used in the non-bonded energy calculation.

`CHARGE'

The charge of the atom.

`POLAR'

The polarizability of the atom as used in the non-bonded energy calculation.

`NEFF'

The effective number of electrons as used in the non-bonded energy calculation.

`VSGEPOL, ASGEPOL, MSGEPOL'

These three table properties use the GEPOL algorithm²³⁴⁵ to calculate three different surface properties of the atoms; van der Waals, accessible, and molecular surfaces. The van der Waals surface (keyword VSGEPOL) is the surface of the atoms calculated using the van der Waals radii and accessibility is ignored. The accessible surface (keyword ASGEPOL) is the area of the locus of the center of water probe. It is the same surface as calculated by the Lee and Richards algorithm referenced above. The molecular surface (keyword MSGEPOL) is the locus of points on the surface of the probe sphere when the probe is in contact with at least one atom in the molecule.

When calculating van der Waals and accessible surfaces, the GEPOL algorithm uses a points on tesselated sphere to calculate what parts of the sphere are exposed, and it adds all the contributions of the tesserae to determine the surface. The calculation of the molecular surface uses this accessible surface algorithm, but additional spheres are added to the calculation of the accessible surface, and these additional spheres closely define the molecular surface.

The GEPOL command, see Gepol Command, may be used to set operating parameters for the GEPOL algorithm.

`RVSGEPOL, RASGEPOL, RMSGEPOL'

These three table properties are the “relative” equivalents of VSGEPOL, ASGEPOL, and MSGEPOL. In this context, “relative” means relative to the surface area of a sphere of radius equal to the atomic radius in the case of the van der Waals surface and molecular surface, and relative to a sphere of radius equal to the atomic radius plus the solvent probe radius in the case of the accessible surface.