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Building Hydrogen Positions

The hbuild statement tries to build the position of any selected hydrogen based on the position of the heavy atom antecedents (Brünger and Karplus, 1988). It works in a general way and can be used with any empirical force field. It performs local energy minimization in cases where the placement of the hydrogens is not unique. Waters close to the macromolecule are placed first, followed by waters that are farther away. Several iterations can be carried out to reach self-consistency. The minimization uses the energy function (Eq. 4.1) except that the specification of constraints interaction statements (Section 4.7) are ignored.

The hydrogen building facility does not use the improper or dihedral information in the topology file (Section 3.1.1). The chirality of methyl and methylene groups is determined by the order of four substituents to the central carbon atom as specified in the molecular structure. By changing the order in which the atoms are defined in the residue statement (Section 3.1.1), the chirality of the center is changed.

Hydrogens are recognized by X-PLOR by their mass. All atoms with a mass less than 3.5 amu are considered hydrogens. Certain simulated annealing protocols (e.g., Section 38.3.3) make use of artifically increased masses. If hydrogen building is employed in these protocols, the hydrogen building routine will return an error statement. In this case the user has to reset the mass of the hydrogen atoms to their physical values.

To save CPU time, it is suggested to carry out the hydrogen building without nonbonded energy terms. The coordinates then will need minimization to relieve possible bad contacts between the initial hydrogen placements.

Subsections

Xplor-NIH 2025-03-21