SYBYL MOL2 format

This format is used for general molecule input and output of dock. Although previous versions of dock supported an extended PDB format to store molecule information, the current version now uses MOL2 as the primary molecule format. This format has the advantage of storing all the necessary information for atom features, position, and connectivity. It is also a standardized format that other modeling programs can read.

Specification

Please refer to sybyl documentation for format specifications.

Of the many record types in a MOL2 file, dock recognizes the following: MOLECULE, ATOM, BOND, SUBSTRUCTURE and SET. In the MOLECULE record, dock utilizes information about the molecule name and number of atoms, bonds, substructures and sets. In the ATOM record dock utilizes information about the atom names, types, coordinates, and partial charges. In the BOND record, dock utilizes the atom identifiers for the bond. In the SUBSTRUCTURE record, dock records the fields, but does not utilize them. The SET records are entirely optional. They are used only in special circumstances, like when Ligand Flexibility is considered..

Example

This example file illustrates all the elements of the MOL2 file read and written by dock. It includes optional SET records which are used by the Ligand Flexibility routines.

 

@<TRIPOS>MOLECULE

Histidine

20 20 1 0 2

SMALL

GASTEIGER

****

Histidine with Main Chain as Rigid Anchor

@<TRIPOS>ATOM

1 N1 -1.0947 0.5371 1.7186 N.4 1 <1> 0.2252

2 C2 -0.9885 0.9170 0.2765 C.3 1 <1> 0.0213

3 C3 -0.2043 -0.1565 -0.4766 C.3 1 <1> 0.0354

4 C4 -2.3725 1.0376 -0.3154 C.2 1 <1> 0.0897

5 O5 -2.7546 2.1336 -0.8057 O.co2 1 <1> -0.5442

6 C6 1.1797 -0.2771 0.1153 C.2 1 <1> 0.0328

7 N7 2.2791 0.4215 -0.2757 N.pl3 1 <1> -0.3074

8 C8 1.5387 -1.0911 1.1173 C.2 1 <1> 0.0462

9 C9 3.3256 0.0285 0.4990 C.2 1 <1> 0.0853

10 N10 2.9039 -0.8872 1.3511 N.2 1 <1> -0.2465

11 H11 -1.6259 1.2643 2.2287 H 1 <1> 0.2001

12 O12 -3.1452 0.0423 -0.3188 O.co2 1 <1> -0.5442

13 H13 -0.1461 0.4545 2.1242 H 1 <1> 0.2001

14 H14 -0.4726 1.8710 0.1898 H 1 <1> 0.0918

15 H15 -0.7202 -1.1105 -0.3899 H 1 <1> 0.0385

16 H16 -0.1270 0.1200 -1.5261 H 1 <1> 0.0385

17 H17 2.3126 1.1114 -1.0125 H 1 <1> 0.1528

18 H18 0.8943 -1.7774 1.6466 H 1 <1> 0.0845

19 H19 4.3357 0.4040 0.4286 H 1 <1> 0.1000

20 H20 -1.5855 -0.3703 1.8010 H 1 <1> 0.2001

@<TRIPOS>BOND

1 1 2 1

2 2 3 1

3 2 4 1

4 3 6 1

5 4 5 ar

6 6 7 1

7 6 8 2

8 7 9 1

9 8 10 1

10 9 10 2

11 1 11 1

12 4 12 ar

13 1 13 1

14 2 14 1

15 3 15 1

16 3 16 1

17 7 17 1

18 8 18 1

19 9 19 1

20 1 20 1

@<TRIPOS>SUBSTRUCTURE

1 **** 1 TEMP 0 **** **** 0 ROOT

@<TRIPOS>SET

ANCHOR STATIC ATOMS <user> **** Anchor Atom Set

1 2

RIGID STATIC BONDS <user> **** Rigid Bond Set

2 1 3

UC Regents 1998
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