Completing a Partial Structure

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.