A partial structure is one where some of the atoms have defined positions and
the rest are unknown. If the structure was generated with preammp the unknown
atoms will be at the location 0,0,0. In order to build a full structure it is
necessary to constrain or restrain the known structure and then build in the
new atoms. The command "tether all force_constant;" will generate a set of
harmonic restraints ("tethers") for the current known atoms. If you use tethers
remember to activate them. It is more efficient to use constraints. These can be set with the command
"nzinactive low_atom high_atom ;" (i.e. "nzinactive 0 100000000;").
In either case, the new atoms must first be moved to approximate positions
before the structure can be optimized. If the new atoms are mostly hydrogens use
only the bond and angle potentials and conjugate gradients. If there are extensive additions GSDG is a better choice. Chiral hydrogens are best placed by using only the hybrid terms after having built an approximate structure and then using hybrid bond and
angle to generate a more correct structure. Prochiral hydrogens require special
calculations; an example can be seen in the vlfix.amp script.
Once the approximate structure has been built remove the constraints with
"active low_atom high_atom;" (i.e. active 0 100000;) or by deactivating the
tethers, and optimize the whole structure.