Topology.append() — append residue topology library

append(file)

This command reads residue topologies from the topology library given by file, such as the CHARMM 22 topology file [MacKerell et al., 1998]. 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. To define your entries in the topology library, see the FAQ Section 3.1, Questions 8 and 9.

file can be a filename or a readable file handle (see modfile.File()).

This command also sets Topology.submodel appropriately to match the topology library, assuming a suitable header is found in the library file (see Topology.submodel). For example, the default topology for comparative modeling by MODELLER includes only non-hydrogen atoms (Topology.submodel = 3).

The new residue topologies are added to the existing residue topologies. (To replace the old topology, call Topology.clear() first.) 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 Topology.make() command.

Example: See model.patch() command.