Maestro User Manual

Appendix A: The Maestro File Format

Maestro 10.2 User Manual

421

    s_m_grow_name

The name used by the Maestro structure builder.

    i_m_atomic_number 

The atomic number.

    i_m_formal_charg

The formal charge.

    i_m_representation

The representation used to draw this atom.

    i_m_visibility

A flag to indicate whether this atom is

displayed in Maestro or not.

    s_m_atom_name 

The user-specified atom name.

    :::

The separator for the end of the data items.

Next follow the data values. The first column contains an index number that is assigned automatically. 

Remaining columns represent the data values in the same order as data names given above.

1   3   0.547623     1.262401   -0.990300    1 " " X " "     2   0.00000   

0.00000 CHEX "    " "    "      6   0   0  1   ""

2   3   -0.930177    1.296701   -1.411700    1 " " X " "     2   0.00000   

0.00000 CHEX "    " "    "     6   0   0  1   ""

3   3   -1.821477    1.772701   -0.253300    1 " " X " "     2   0.00000   

0.00000 CHEX "    " "  c1"   6   0   0  1   ""

4   3   -1.624777    0.890901    0.990300     1 " " X " "    2   0.00000    

0.00000 CHEX "    " "    "     6   0   0  1   ""

    ....

17  41  0.493223   -0.677999   0.001900   1 " " X " "   21   0.00000   0.00000 

CHEX "    " "  n3"    1  0  0   1   ""

18  41  1.817023    0.395501   0.566000    1 " " X " "   21   0.00000   

0.00000 CHEX "    " "  n2"   1   0  0  1   ""

    ::: 

The separator for the end of the data values.

}

The end of the atoms block.

        m_bond[36] { 

The bond block. There are 36 bonds.

    i_m_from

The atom the bond is from.

    i_m_to

The atom the bond is to.

    i_m_order

The bond order.

    i_m_from_rep

The graphical representation for the “from” half-bond.

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Appendix A: The Maestro File Format

Schrödinger Software Release 2015-2

422

    i_m_to_rep

The graphical representation for the “to” half-bond.

    :::

The end of the data names for bond data.

What follows are the data items for the bond block. The first column contains an automatically 

assigned index number for each item.

    1   1    2   1 1 1

    2   1    6   1 1 1

...

    35  17   6   1 1 1

    36  18   6   1 1 1

    :::

The end of the bond data items.

  }

The end of the bond block.

}

The end of the CT block.

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Appendix B

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423

Maestro User Manual

Appendix B:

Atom Types

Maestro atom types are not “hard-wired” into the program, but are read in at run-time from a

file called atom.typ, which is installed in $SCHRODINGER/mmshare-vversion/data. We

continue to use the original MacroModel atom types for most applications, but now have a

mechanism for easily adding new types. 

You can add your own atom types and supply parameters for these types in the force-field file.

The default atom.typ file is the one located in $SCHRODINGER/mmshare-vversion/data. A

local file of this name overrides the default, as does a local file whose name is filename.typ,

where filename is the stem of the filename.mae file. This system of default version with local

overrides is analogous to that used for force field and solvation files.

Currently Maestro accepts atom types up through number 300. We restrict the type numbers

that we supply to the range 0 through 199. When adding your own types, you should begin

with the number 200. Negative atom types are not accepted.

Inside Maestro you can change atoms in existing structures to new types, including user-

defined types. However, no provision is made in the current version for the builder to obtain the

geometric information it needs from the atom.typ file, which would require extensions to the

format of this file. Also, the original atom types remain “hard-wired” in Maestro. Therefore,

you should not attempt to redefine types which we supply. Instead, add new types. The

atom.typ

 file itself contains comments describing its format and usage.

The atom types and their equivalents in other force fields are listed in 

Table B.1

 and 

Table B.2

.

These atom types are defined in the atom.typ file. Note that 00 atoms are stored as type 0 in

the atom connection table, and that all current force fields require explicit hydrogens on hetero-

atoms.

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Appendix B: Atom Types

Schrödinger Software Release 2015-2

424

Table B.1. Atom types and equivalents. 

No.

Symbol

Description

Equivalencies

MM2/

MM3

Charmm

Amber

 1

C1

Carbon - sp 

 2

C2

Carbon - sp

2

 2,3

CT,C

C, 

C*, 

CA, 

CB, CC, CM, 

CF, CG, CN

 3

C3

Carbon - sp

3

 

1

CT

CT

 4

CA

United atom CH - sp

3

CH1E

CH

 5

CB

United atom CH

2

 - sp

3

 CH2E

C2

 6

CC

United atom CH

3

 - sp

3

CH3E

C3

 7

CD

United atom CH - sp

2

CR1E

CD, CE, CJ, 

CP

 8

CE

United atom CH

2

 - sp

2

 9

CF

United atom CH - sp

10

CM

Carbanion (C

–

)

11

CP

Carbocation (C

+

)

30

12

CR

Carbon free radical

29

...

14

C0

Any carbon

15

O2

Oxygen - double bond

7

O

O, O2

16

O3

Oxygen - single bond

6

OH1, OH2

OS, OH 

17

OA

United atom OH

OH1E 

18

OM

O

−

 (alkoxide, carboxylate)

47

OC 

19

OW

United atom H

2

O OH2E

20

OP

Oxonium (sp

2

) =[O

+

]–

21

OQ

Oxonium (sp

3

) R

3

O

+

...

23

O0

Any oxygen

24

N1

Nitrogen - sp

10

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