Prime User Manual - ISP

112
Chapter 11: Command Syntax
11.9 tfm—Tertiary Folding Module
The tfm program generates one or more complete backbone conformations starting from a
primary sequence and secondary structure, along with optional domain boundaries and sheet
topologies. In addition, tfm can accept several different types of constraint including multiple
coordinate templates, multiple types of distance constraints, and dihedral angle constraints. A
large number of run-time parameters allow the code to be used in a variety of ways, from minimizing
a homology model to full ab initio folding.
Syntax
The tfm program has hundreds of user-specified options contained in over a dozen input files.
A detailed description of all the options is beyond the scope of this document. The refine
command can be used as a wrapper to prepare default input files. If suitable input has been
prepared, there is also a top-level wrapper for tfm that can be used to run the program directly
under Schrodinger Job Control. It can be invoked from the command line via:
$SCHRODINGER/tfm input-file [options]
where input-file is typically the job name, with or without a .inp extension. The input file
must be either the first or last command-line argument, and everything else on the command
line is passed as is to Job Control.
Options
All options are specified in the input file, and there are no command-line options, other than
those recognized by Job Control.
Command Input File
There are only three keywords recognized in the command input file, listed in Table 11.12.
Table 11.12. Keywords for tfm program.
Keyword Description
INPUT_FILE filename The input file passed to the executable.
OUTPUT_FILE filename The output produced by the executable.
STRUCT_NAME name Optional. Prefix for files in the local directory that will be automatically
treated as input, such as template or constraint files.
Prime 2.1 User Manual