ADL: map

Florenci Vicent González Adelantado fgonzale at qio.uji.es
Thu Jan 31 12:14:24 PST 2008


Ruth,
thanks for your message, I am glad to hear it from you. In my case, there is a
sulfur in the flexible sidechain but there is not any sulfur in the ligand. I
hope you will be able to fix it, so far I fixed it creating a fake file by
copying "Enzyme_rigid.OA.map" and changing letters,I know that is wrong but at
least I was able to get my first (although wrong) docking.

Floren



Mensaje citado por Ruth Huey <rhuey at scripps.edu>:

> Hi Floren,
> 
> Probably you have run into this problem because the atom type SA was 
> missing from the ligand_types entry in the grid parameter file you used 
> for the autogrid4 calculation and/or from the  ligand_types entry in the 
> docking parameter file you used for the autodock4 calculation.
>  
> Unfortunately, there is currently a bug in ADT which affects the setup 
> of input files for dockings involving flexible sidechains in the 
> receptor. Specifically:
>     If there are some atom types in ligand which are not also in the 
> atom types of the flexible sidechains and if the ligand is specified 
> (Docking->Ligand->) before the flexible residues file 
> (Docking->Macromolecule->), potentially these types may be missing from 
> the dpf. 
> 
> I am currently working on this issue but have not yet discovered a 
> robust solution....
> 
> Meanwhile, you should check the completeness of the 'ligand_types' and 
> 'maps'  in the input dpf files.
> 
>      Ruth
> 
> Florenci V. Gonzalez wrote:
> > Hello all,
> > 	when I launch the docking it stops because it cannot find 
> > the  "Enzyme_rigid.SA.map" file.
> > I do not know why it does not create that file if the SA is an atom type.
> >   Can anyone help me on this?
> >
> > Thanks,
> >
> > Floren
> >
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> >
> >   
> 
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