To create a new molecule you have to first define a template. You then run preammp. When preammp asks for a coordinate set dont enter
any file name. Unlike with the existing molecule case, preammp will not be able
to automatically look up the kind of molecule from the coordinates. So you
will be prompted to enter a molecule name. This is limited to three characters to
fit into PDB format. (Sorry about that, but that is how it is).
It is then necessary to build the molecule. Preammp outputs 0,0,0 for x,y,z
so all of the atoms are in the same locations. This means you cannot just "turn
on" minimization. For small simple molecules, use gsdg to build an initial self-avoiding, but distorted structure and then use conjugate gradients to polish it up. More complicated molecules will require embedding or
homotopy approaches, and possible manual intervention. Polymers, such as proteins,
will require that an initial model be built with just the bond and angle terms. Set the torsion angles to generate an extended structure and then use other data such as NOE
distance terms to fold the polymer.