Molfiles: V3000 and V2000

Molfiles: V3000 and V2000

The CT file format (https://discover.3ds.com/ctfile-documentation-request-form) specifies 2 versions of the molfile:
v2000 is an older format that is more widely understood. It also limits the number of atoms to 999. An example of a V2000 mofile:

  ACCLDraw04262113072D


  4  3  0  0  0  0  0  0  0  0999 V2000
    4.3750   -4.2813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3979   -3.6907    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3979   -2.5092    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4210   -4.2814    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
M  END

V3000 has only been around since 1995 and is not supported by every piece of software that handles V2000. It allows arbitrarily large structures and supports additional features. An example of a V3000 molfile:

  ACCLDraw04262113142D

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 4 3 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C 4.375 -4.2813 0 0 
M  V30 2 C 5.3979 -3.6907 0 0 
M  V30 3 O 5.3979 -2.5092 0 0 
M  V30 4 O 6.421 -4.2814 0 0 
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2 
M  V30 2 2 2 3 
M  V30 3 1 2 4 
M  V30 END BOND
M  V30 END CTAB
M  END

Officially, GSRS only supports V2000 molfiles. However, you may be able to use V3000 molfiles if your GSRS instance is using the underlying CDK option. You force the use of CDK by adding this option to the command that starts GSRS:

-Dmolwitch=CDK

Note: you'll need to run JCHEM or CDK consistently. (Switching back and forth between JCHEM or CDK will lead to inconsistent values in your index.