[Dock-fans] sdf to mol2 with omega

Gareth Williams gareth.2.williams at kcl.ac.uk
Thu Apr 21 05:10:41 PDT 2005

I'm trying to generate a ligand database for DOCK. For this I need to 
convert a sdf file to a mol2 file (I haven't git access to SYBYL). I ran 
openeye OMEGA with maxconfs set to 1 and got a mol2 file. However, DOCK 
needs a substructure entry, which is absent in the OMEGA output. The 
substructure entry comes after the bond data and is like:

  1      BENZENE 1       PERM    0       ****    ****    0       ROOT

I've been trying to add a substructure entry without success. Does anyone 
know what the minimal entry requirement is? I assume that DOCK does not 
need the substructure information.

Any help appreciated.

Gareth Williams
Wolfson CARD
The Wolfson Wing
Hodgkin Building
Kings College London
London SE1 1UL
Tel:  020 7848 6806
Fax: 020 7848 6816

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