Maestro User Manual

Appendix C: Substructure Notation

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N0=C0-C0=C0-C0=C0(-1)-C0=C0-C0=C0-5

In this pattern, the atom types are general and the bond orders are exact. Thus, this pattern

specifies an exact resonance form, and that is the only form it will match. 

As an alternative, atom types are often specified more exactly, to designate the atomic hybrid-

izations, and wildcard bonds are used for the connectivity. For quinoline, this kind of specifica-

tion could look like the following:

N2*C2*C2*C2*C2*C2(*1)*C2*C2*C2*C2*5

This pattern matches any resonance form of quinoline.

Each pattern indicates a simple ring closure in branch parentheses, in the middle of the pattern.

Strictly speaking, the parentheses are not needed, since the ring closure is a branch by defini-

tion. Also, since the ring closure introduces no new atom, it doesn’t really need to be shielded

from bonding association with the symbol after it. However, we recommend use of parentheses

in such cases, to keep it clear that the atoms on either side of the ring closure indication are

bonded to each other.

C.7

Formal Charge Extensions

The  mmsubs notation has syntax to explicitly specify formal charge on an atom, separately

from what the atom type itself implies. This is an extension over the MacroModel notation.

Formal charges can be specified for any MacroModel atom type, but the usage makes the most

sense when applied to a wildcard atom type. The syntax is as follows:

i. Formal charges are specified using the {} braces after an atom type symbol. The symbols

“+”, “-”, and “0” are used to represent positive, negative, and no charge. Examples:

C0{+}

  —  any carbon with a +1 charge

N0{-}

  —  any nitrogen with a -1 charge

O0{0}

  —  any neutral oxygen

ii. An integer in the range 1-9 can be used to specify the number of formal charges:

N0{1+}

  —  any nitrogen with a +1 charge

S0{2+}

  —  any sulfur with a +2 charge

iii. A question mark ? can be used to indicate any number (1 or more) of a particular charge

type:

N0{?+}

  —  any nitrogen with any positive charge

C0{?-}

  —  any carbon with any negative charge

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Appendix C: Substructure Notation

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It is possible to create paradoxical specifications:

CP{-}

  —  negatively charged CP (atom type for carbocation)

OM{+}

  —  positively charged OM (type for oxygen with -1 charge)

These would not be rejected as erroneous, but it is impossible for them to ever match anything.

Formal charge syntax is especially useful in atom-typing rules.

C.8

Atom Type Equivalence Labels

The mmsubs software supports the use of atom type equivalence labels in substructure patterns.

Such labels are defined in a data file with a simple text format, for example:

# Comments begin with a "#"

CS  CA CB CC

CT  CA CB CC C3

CU  C2 CD CE

CH  CA CB CC C3 H1

The equivalence label comes first, followed by the atom types to be made equivalent, separated

by commas or spaces. Wildcard atom types are permitted, but formal charge specifiers are not.

Equivalence labels take precedence over standard atom type symbols. Equivalence labels

cannot be defined recursively.

With the assignments shown above, if an mmsubs pattern contains the equivalence label CT, it

will match an atom of type CA, CB, CC, or C3.

Some of the labels in this example collect united atom types with non-united types, for equiva-

lent treatment in mmsubs patterns. This is clearly useful in contexts where molecule connec-

tion tables might have either form. 

Any number of equivalence labels can be defined. As with standard atom type symbols, char-

acter case matters in the equivalence labels, and every label must have 2 characters. The first

character is conventionally a letter; a number may be used but is not encouraged.

The default equivalence labels are defined in a data file installed with the Schrödinger software

in 

$SCHRODINGER/mmshare-vversion/data/mmsubs.ini 

If you want to augment or override the default equivalence labels, you can copy the installed

mmsubs.ini

 file and edit it. To define equivalence labels for all applications, save the copy in

$HOME/.schrodinger/mmshare

. To define equivalence labels for a particular application,

save the copy in the directory from which you run the application. 

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Appendix C: Substructure Notation

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C.9

Differences between mmsubs and bmin notations

For the record, here are the known technical differences between the mmsubs and bmin nota-

tions --

• In MacroModel notation, a pattern is limited to at most 50 atoms, and a maximum of 130

characters. In mmsubs notation, there is no explicit limit on the number of atoms in a pat-

tern, though there is a limit on the pattern specification itself of about 10,000 characters. 

• In MacroModel notation, the wildcard bond order symbol * does not cover zero-order

bonds. In mmsubs notation, it does.

• The MacroModel notation has no syntax for explicitly specifying formal charges. 

• In MacroModel notation, equivalence labels are defined in force field data files. In

mmsubs

 notation, equivalence labels are defined in a distinct data file.

• In MacroModel, wildcard atom type symbols are not permitted on the right-hand side of

equivalence label definitions. 

C.10 Related Files

The data file that formally specifies MacroModel atom type symbols is installed in the

Schrödinger software installation at the following location:

$SCHRODINGER/mmshare-v

version/data/atom.typ

Details of the atom types are given in this file. Further information on the atom types can be

found in the atom-typing rules file, which is installed at the following location:

$SCHRODINGER/mmshare-v

version/data/mmatype.ini 

This file uses the mmsubs notation to define the rules. 

Another related file is the file that defines the default equivalence labels that can be used in

mmsubs patterns,

$SCHRODINGER/mmshare-v

version/data/mmsubs.ini

You may on occasion need to override this installed file with your own customized version.

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