[Dock-fans] sdf to mol2 with omega

Terry Lang terry at cgl.ucsf.edu
Thu Apr 21 13:24:19 PDT 2005


Dear Gareth,

   The entry you have below looks fine, but you also need to modify the 
line at the top of the file that indicates how many entries are in each 
section (two lines after the @<TRIPOS>MOLECULE).  The format of the line is:
  #_of_atoms  #_of_bonds #_of_substructures #_of_features #_of_sets

For example, the section might look like this for a ligand:

@<TRIPOS>MOLECULE
****
         20      20      1       0       0
SMALL
GAST_HUCK

Hopefully, this will take care of your problem,
Terry


At 05:10 AM 4/21/2005, Gareth Williams wrote:
>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:
>
>@<TRIPOS>SUBSTRUCTURE
>  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
>http://www.kcl.ac.uk/depsta/biomedical/CARD/CARD.htm
>
>
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P. Therese (Downing) Lang
Kuntz and James Labs
UCSF - CCB Graduate Program
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