[Dock-fans] ligand file input

John J. Irwin jji at cgl.ucsf.edu
Mon Jul 16 10:29:50 PDT 2007


Hi Loraine

As a general rule, if the atom type changes enough to give it a new
AMBER atom type (e.g. C sp2 changes to C sp3) then DOCK results may be
different due to different VDW parameters.

Specifically, you have a bigger problem, as the first "C1" seems to be
hexavalent. and the second "C1" seems to be pentavalent. There is also a
hexavalent N. We recommend OEChem from OpenEye for converting file formats.

Good luck!

John


BRILLET Loraine 216515 wrote:
>
> Dear all,
>
>  
>
> I have noticed that the Tripos mol2 atom/bond types given to ligands
> when converting them to mol2 format depend on the program used to do
> that. For example, I used Chimera and OpenBabel to prepare the mol2
> file for nocodazole (adding H and partial charges). You can see that
> the atom/bond types are different (see files included).
>
> Do these different atom/bond types have an influence on the docking
> results with DOCK?
>
>  
>
> Regards,
>
>  
>
> Loraine Brillet
>
>  
>
>  
>
>  
>
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>
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