Add Hydrogens
Previous  Top  Next

Dialog Box - called from: Atoms Dialog

This option currently will attempt to identify carbon, nitrogen and oxygen atoms which should have hydrogen attached. These atoms must have atom types 6, 7 and 8 respectively.

The first option will actually add hydrogen atoms to the list of input atoms - the new H atoms will immediately follow the atom to which they are added.

The second option, "Change types..." will not actually add atoms, it will simply change the atom type of the H-deficient atom to indicate the deficiency. The type number of carbon atoms will be changed from 6 to 106, 206 or 306 respectively if the atom lacks 1, 2 or 3 hydrogens and similarly for N and O. This option is intended specifically for files which will be imported into the program VIBRATZ, and for vibrational models in which the weights of the C, N or O atoms are "corrected" for the attached hydrogens, rather than dealing with the H atoms explicitly.

Orientation. When adding two hydrogens to a double-bonded carbon or to a nitrogen the orientation is quasi-random with respect to rotation about the other bond vector, and likewise when adding three hydrogens to a singly-bonded carbon atom. When adding one H to an oxygen atom the orientation of the plane of the X-O-H angle is also quasi-random. "Quasi-random" means that the hydrogens are added in a fixed orientation with the C-X vector (if the atom in question is a carbon) rotated to [001], then the group is in effect rotated back to its actual orientation in the structure. H2O groups (water) are fully random in that two random rotations are applied.

Symmetry. The generated hydrogen atoms may not be consistent with symmetry, which will be indicated by an excess number of H atoms in the complete structure.

At this time the algorithms for locating hydrogens are very simple, based only on the number of atoms and bond lengths in the first coordination sphere. The procedure was developed specifically for protein structures where there are only a limited number of configurations of nitrogen in particular. The algorithms may be corrected and expanded as necessary. If the hydrogen location in a structure is incorrect or ambiguous, please send the structure file (.str file) to support@shapesoftware.com, with a list of the input atoms, by number if necessary, which are believed to be incorrect.