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Chapter 4
Template-Based Approach
4.1
Introduction to templates
SMOG v2 offers increased versatility over SMOG v1 [9] by shifting to a template-based
approach for defining molecular structures. Each template allows for direct control of
the structure-based energy function, which may include (but is not limited to) multiresolution models, and models that include non-specific interactions. The plug-and-play
nature of the templates has the additional advantage of forcefield portability and easy
sharing of user-created variations of structure-based potentials.
A single SMOG “template” is comprised of four XML-formatted files. These files are
absolutely necessary when using SMOG v2. XML format was adopted because of its
consistent formatting, ease of editability and readability, and there are widely available
program modules to generate, and parse XML files. Furthermore, XML allows for
schemas, a form content format restriction file, to which the template files must conform,
which adds an additional layer of error checking capabilities. This chapter assumes that
the user knows the basics of XML formatting. Users unfamiliar with XML formatting
may want to check out the W3schools’ website.
Table 4.1 summarizes the purpose of each template file. In Chapter 5, we show how to
add new new residue to the template files for an All-Atom structure-based model.
4.2
SMOG v2 Templates
SMOG v2 expects four template files to be present in a single folder (i.e. the template
folder). As discussed in Chapter 3, the template folder name is a required argument
when running SMOG v2. A template folder can only contain one of each file type. If
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