[Dock-fans] de novo Dock (beta) problems

Robert C. Rizzo rizzorc at gmail.com
Fri Jul 6 08:10:43 PDT 2018

Dear Gyorgy,

Thanks for being one of the first de novo DOCK testers.

During development we primarily used MOL2 files from the ZINC database to
generate fragment libraries.  I also believed that we have tested MOL2
files generated by he program MOE and AMBER.  In principle however, DOCK
should be able to process any MOL2 file for fragment library generation as
long as it is in a standard format.  For example, the files should be in a
reasonably 3D conformation, with hydrogen atoms, contain partial atomic
charges, and it should contain standard SYBYL atom types.  The atom types
in particular will influence how the fragments are created.  So, I would
suspect that in the case in which you used different SMILES strings to
create different MOL2 files, and obtained different fragments libraries,
that changes in atom typing may be the culprit.

In terms of some atoms not being recognized (B, Ca, Co,Gd) this is to my
knowledge a general issue with DOCK, and not necessarily related to de novo
DOCK or NOVA (not all atom types are supported at this time).

As Scott indicated earlier, after double checking the sanity of your MOL2
files, please send us the MOL2 file that makes DOCK crash and we will

Hope this helps,

Robert C. Rizzo, Ph.D., Professor
Department of Applied Mathematics & Statistics,
Institute of Chemical Biology & Drug Discovery,
Laufer Center for Physical & Quantitative Biology
Stony Brook University
Stony Brook NY, 11794-3600
Cell: (631) 944-2891
Office: (631) 632-9340
Fax: (631) 632-8490
rizzorc at gmail.com

On Thu, Jul 5, 2018 at 4:55 PM, Scott Brozell <sbrozell at rci.rutgers.edu>

> Hi,
> Thanks for the feedback.
> 1.  Can you send me a self contained set of input files to
> reproduce the crash ?
> Someone will be in contact regarding the other issues.
> thanks,
> scott
> On Thu, Jun 28, 2018 at 12:19:47PM +0100, Gyorgy Abrusan wrote:
> > I have encountered the following problems with de novo dock
> >
> > 1. fragment library generation:
> > a) if I convert the entries of drugbase from sdf to mol2 (with
> openbabel),
> > dock crashes, and is unable to build the libraries
> > b) several atoms present in drugbase (and pdb ligands are not recognized
> ,
> > e.g. B, Ca, Co,Gd)
> >
> > 2. NOVA algorithm.
> > It does seem to make a big difference how I create the fragment
> libraries.
> > 1) If convert canonical smiles from CACTVS to mol2 and use them for
> > fraglib, the nova algorithm works and appear to generate valid ligands.
> > 2) if I use different smiles to generate mol2, fragment library
> generation
> > is successful, but the nova algorithm does not seem to work with these
> > libraries, and I get the error message that no anchors were found.
> >
> > (I used openbabel for all conversions)
> >
> > So I would like to ask for some advice about the recommended way of
> > creating fragment libraries.
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