How do I add fragments to the Build panel fragment library?

You can add custom fragments by modifying Maestro's .bld files. All these files are stored in $SCHRODINGER/mmshare-vversion/data/res. Generally, we recommend that you make changes only in local copies of the build files, so that the the modified files will only be used when you run Maestro, not other users. To do this, copy the files you would like to modify to your user resources directory ($HOME/.schrodinger/maestroNN directory on Linux or %APPDATA%\Schrodinger\maestroNN on Windows). On Linux, you can also copy the files to some other directory, and Maestro will use the modified files whenever it is started from that directory.

To add a fragment to the organic fragment library:

1. Copy $SCHRODINGER/mmshare-vversion/data/res/organic.bld to a local directory.
2. Use Maestro to build the desired fragment.
3. Use the Atom Properties tab of the Build panel to assign appropriate grow names to the atoms. (Rules for assigning grow names for organic fragments are included below).
4. Use the controls on the Atom Properties tab of the Build panel to set all atom-based properties (color, PDB atom and residue name) as they are intended to appear in the structures built with this fragment.
5. Save the structure as its own Maestro-formatted file. Then in a text editor, open the file and remove the segment that appears between the first set of brackets ({}) at the beginning of the file. Copy the remainder of the text in the file to the end of the organic.bld file.
6. Restart Maestro. The new fragment should appear at the end of the fragment list in the "Organic" section of the Fragments tab within the Build panel. The new fragment is now available for use in building operations, and the fragment should behave the same as the standard fragments.

Grow Name Rules:

For each fragment, two sets of grow names are assigned. Each grow name consists of a letter, indicating grow name type, and a number, indicating bond direction.

The first set of grow names, called the "connect" names, dictates the orientation in which the fragment will be connected to an existing structure in the Workspace. "Connect" grow names begin with "c" and include a number between 1 and 3.

The second set of grow names, called the "new" names, is used only when building in "Grow" mode. New grow names specify where in the fragment a new grow bond will appear once the fragment has been added to an existing Workspace structure. New grow names begin with "n" and also include 1, 2, or 3.

When building using fragments from the Organic fragment library, atoms that are labeled with a "2" (c2, n2) will be replaced during grow or attach operations. For example, when growing an alkene onto an existing structure, the hydrogen labeled as "c2" is removed, and a new second order bond is formed between the atom in the existing structure currently defined as the grow bond head and atom "c1". A new grow bond then appears between "n1" and "n2" of the alkane fragment.

The "c3" and "n3" labels are used in grow rules that dictate the geometry about the bond that is formed during growing operations. Most fragments have an atom labeled "c3" attached to "c1" and an atom labeled "n3" attached to "n1".

Keywords: Maestro, build, fragments

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