Reactor, export to mol2 or 3D format problem

Hi,

I have some a list of molecules in mol2 format in a single file. I want to run a reaction over them and get the results in mol2 format or another 3D format. However, I tried different ways, and it seems that I am only able to obtain mol format as output (I do not see the mol2 option for the output). And for the mol option everything seems to be "plane" or in a 2D output like:

 

  41 MOL                               0
   1   2  -7.6977   0.0397   0.0000C
   2   2  -6.3631   0.8081   0.0000C
   3   2  -5.0303   0.0365   0.0000C
   4   2  -5.0321  -1.5035   0.0000C
   5   2  -6.3667  -2.2719   0.0000C
   6   2  -7.6995  -1.5003   0.0000C
   7   8  -8.8452  -2.5294   0.0000O
   8   1  -8.2205  -3.9370   0.0000C
   9   8  -6.6887  -3.7778   0.0000O
  10   1  -3.7031   0.8081   0.0000C
  11  13  -3.3277  -0.2152   0.0000H

......

 

So could anybody help to me?

 

Thanks in advance

 

 

Hi,

Do you use Reactor GUI, or command line? In command line you can simply specify the "mol2" output format with the "-f" switch:

$ react -r "[Cl:4][C:3]=O.[#7:2][H:1]>>[#7:2][C:3]=O.[Cl:4][H:1]" "CCCC(Cl)=O" "NCCC1CCCCC1" -f mol2

@MOLECULE



14 14

SMALL

USER_CHARGES

@ATOM

1       C1    -6.6684    -5.3900     0.0000     C.3     1       noname  -0.0649

2       C2    -5.3347    -6.1600     0.0000     C.3     1       noname  -0.0479

3       C3    -4.0010    -5.3900     0.0000     C.3     1       noname  0.0209

4       C4    -2.6674    -6.1600     0.0000     C.2     1       noname  0.0372

5       O1    -2.6674    -7.7000     0.0000     O.2     1       noname  -0.2969

6       N1    -1.3337    -5.3900     0.0000     N.3     1       noname  -0.0805

7       C5     0.0000    -6.1600     0.0000     C.3     1       noname  0.0029

8       C6     1.3337    -5.3900     0.0000     C.3     1       noname  -0.0373

9       C7     2.6674    -6.1600     0.0000     C.3     1       noname  -0.0402

10      C8     4.0010    -5.3900     0.0000     C.3     1       noname  -0.0504

11      C9     5.3347    -6.1600     0.0000     C.3     1       noname  -0.0530

12      C10     5.3347    -7.7000     0.0000    C.3     1       noname  -0.0533

13      C11     4.0010    -8.4700     0.0000    C.3     1       noname  -0.0530

14      C12     2.6674    -7.7000     0.0000    C.3     1       noname  -0.0504

@BOND

1       1       2       1

2       2       3       1

3       3       4       1

4       4       5       2

5       6       4       1

6       6       7       1

7       7       8       1

8       8       9       1

9       9       10      1

10      9       14      1

11      10      11      1

12      11      12      1

13      12      13      1

14      13      14      1

@SUBSTRUCTURE

1       noname  1

@MOLECULE



1 0

SMALL

USER_CHARGES

@ATOM

1       Cl1     0.0000     0.0000     0.0000    Cl      1       noname  -0.1465

@BOND

@SUBSTRUCTURE

1       noname  1

I hope this helps.

Zsolt

Hi,

 

no, I am using the GUI

Thank you for reporting this issue, mol2 format is missing from the Standardizer file dialog as well, we will correct these applications in version 5.3. Until that you might use the command line tool.

thanks for the answer.

 

anyway, is it possible to output using the gui to any other 3D format?

The GUI can support all formats that are exportable by the ChemAxon toolkit.
http://www.chemaxon.com/marvin/help/formats/formats.html

Many of these file formats can contain coordinates.