This command reads residue topologies
from the topology library, such as the CHARMM 22 topology file
[MacKerell et al., 1998] (it also reads which subsets of atoms correspond
to each TOPOLOGY_MODEL from library 'MODELS_LIB'). This
file must include atomic connectivities of residues and patching
residues, and the internal coordinates for minimum energy residue
conformations. Patching residues modify residues; for example,
N-terminus, C-terminus and disulfide bonds are defined by patching the
original topology. This information is used for generating the
molecular topology and possibly for calculating an initial
conformation. The default topology for comparative modeling by
MODELLER includes only non-hydrogen atoms (TOPOLOGY_MODEL = 3).
To define your entries in the topology library,
see the FAQ Section 1.9, Questions 17 and
18.
If ADD_TOPOLOGY is on, the new residue topologies are added to the
existing
residue topologies, otherwise the new topology file replaces the old one.
If the topology for a residue is duplicated only the last definition is kept.
Not all the features of the CHARMM 22 topology library are implemented in
MODELLER, although a CHARMM file should be read in successfully. A
variety of topology files for different kinds of models can be
prepared by the MAKE_TOPOLOGY_MODEL command.
The filename for the library is DIRECTORY/FILE.
