The HBUILD command is used to construct positions for hydrogens. Generally, x-ray crystallography cannot resolve the position of hydrogens. However, the position of many of the hydrogens can be determined from the local geometry, e.g. the peptide hydrogen is easy to construct. In other cases, one must examine the local environment to find the best position for a hydrogen, e.g. the position of the gamma hydrogen in serine.
The HBUILD command is a variant of the HBOND command in that it performs a complete determination of all the possible hydrogen bonds with a given set of options, and it uses this set to determine how best to place ambiguous hydrogen positions. This code depends on the current protein topology and parameter files, and will break if the parameter type codes are changed. It will not work with DNA or other molecules.
After using the HBUILD command, it is a good idea to minimize the hydrogen positions only. A sample input follows:
CONS FIX CLEAR ATOM * * H* NOT MINI ABNR NSTEP 250 INBFRQ 25 IHBFRQ 25 CUTNB 8.0 CTONNB 98.0 CTOFNB 99.0