Is there a way that i can ask MODELLER to exactly copy the topology
of backbone,CA atoms of all the aligned residues and model the same
for the other unaligned loop chunks. But it should not add the side
chains. Is there a way that the side chain addition can be stopped
after the desired initial backbone, CA construction.
Modeller can build models using a variety of topologies. The default
topology includes all heavy (i.e. non-hydrogen) atoms. You can change
this by assigning to automodel.toplib. For example,
a = automodel(...)
a.toplib = '${LIB}/top_mnch.lib'
a.make()
will build a model containing only mainchain atoms.
You cannot mix topologies, however (for example, you can't build part of
the model using all atoms, and part with just the backbone).