[Dock-fans] sdf to mol2 with omega

John Irwin jji at cgl.ucsf.edu
Thu Apr 21 14:35:53 PDT 2005


Hi Gareth and Terry

You can use the "addsubstructure.py" python script from the ZINC website, as
contributed by Demer.
http://blaster.docking.org/zinc/fix_substructure.py
The link appears at the bottom of the ZINC main page http://zinc.docking.org
Btw, you shouldn't need the substructure record for DOCK5.2, only previous
DOCK5 and DOCK4 versions.

Good luck!

John



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> -----Original Message-----
> From: dock-fans-bounces at docking.org 
> [mailto:dock-fans-bounces at docking.org] On Behalf Of Terry Lang
> Sent: Thursday, April 21, 2005 1:24 PM
> To: Gareth Williams; dock-fans at docking.org
> Subject: Re: [Dock-fans] sdf to mol2 with omega
> 
> 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
> >
> >
> >_______________________________________________
> >Dock-fans mailing list
> >Dock-fans at docking.org
> >http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> 
> ***NOTE:  This is a new e-mail address (terry at cgl.ucsf.edu)  
> Please update your address book!***
> 
> P. Therese (Downing) Lang
> Kuntz and James Labs
> UCSF - CCB Graduate Program
> Phone:  (415)476-3986
> 
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