BUILD_COORDINATES
Function
Build_Coordinates contains a procedure for building the hydrogen coordinates of a system.
Dependencies
Module | Variables |
CONSTANTS | PI, UNDEFINED |
DEFINITIONS | DP |
IO_UNITS | OUTPUT |
LINEAR_ALGEBRA | CROSS_PRODUCT, NORMALIZE |
RANDOM | RANDOM_VECTOR |
STATUS | ERROR |
ATOMS | Most public items in the module. |
MM_TERMS | Most public items in the module. |
Public Variables
None.
Public Procedures
There is a single public subroutine in this module.
Subroutine | Purpose |
BUILD_HYDROGENS | Build the hydrogen coordinates of a system. |
BUILD_HYDROGENS
This subroutine has no arguments.
Error | Meaning |
Cannot build hydrogen coordinates without appropriate MM definitions. | There is no MM system definition for
the system. |
- BUILD_HYDROGENS builds the missing hydrogen coordinates for a system using a not terribly sophisticated algorithm.
The coordinates of the built hydrogens need to be refined using subsequent constrained minimization and dynamics
calculations.
- Coordinates are taken from the array ATMCRD in the module ATOMS. The position of an atom is taken as missing if one
of its coordinates has the value UNDEFINED from the module CONSTANTS.
- The building algorithm is local and only makes use of information about the coordination geometry of the heavy atom
to which the missing hydrogens are bound.
- An MM system definition is needed for the hydrogens to be built. However, only bond and angle information is used
- no dihedral or non-bonding information.
- The algorithm ignores bonds between hydrogens and will not build hydrogens which are linked to more than one heavy
atom.
- The coordinates of a hydrogen bound to a univalent heavy atom will be added in a random direction.
- The coordinates of a hydrogen bound to a bivalent heavy atom will be added at the appropriate angle to the other
bound atom but in a random plane.
- The coordinates of a hydrogen bound to a trivalent heavy atom are added in the same plane of the remaining atoms,
i.e. the group is assumed to be planar.
- The coordinates of a hydrogen bound to a quadrivalent heavy atom are added in as near a tetrahedral conformation
as possible.
- Hydrogens to heavy atoms with a valency of greater than four are not built.
Stability
Stable although the algorithm could undoubtedly be improved!