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

Scott Brozell sbrozell at rci.rutgers.edu
Thu Jul 5 13:55:35 PDT 2018


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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