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