[Dock-fans] sdf to mol2 with omega

Terry Lang terry at cgl.ucsf.edu
Thu Apr 21 16:16:03 PDT 2005


Actually, in order to run grid, which is a legacy program from DOCK4, you 
do need the substructure.

Sincerely,
Terry


At 02:35 PM 4/21/2005, John Irwin wrote:
>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
>
>
>
>John J. Irwin http://johnirwin.compbio.ucsf.edu
>Adj. Assistant Professor  http://shoichetlab.compbio.ucsf.edu
>Pharmaceutical Chemistry, UCSF, 600 16th St, Suite N474E
>San Francisco CA 94143-2240 USA; Phone +1 415 514-4127 Fax x4260
>
>Free 3D screening database: http://zinc.docking.org. If you are interested
>in new methods of macromolecular crystallography please see the Erice
>Crystallography page http://crystalerice.org. Coming soon:
>2006: Structure and Function of Large Molecular Assemblies
>2007: Engineering of Crystalline Materials Properties
>2008: From Molecules to Medicine - Integrating Crystallography (Drug Design)
>
>
> > -----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
> > >
> > >
> > >_______________________________________________
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> > >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
> >
> > _______________________________________________
> > 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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