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IUPAC naming and partial charge problems on 3D
https://www.dockingserver.com/forum/viewtopic.php?f=3&t=64
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Author:  vittuperkele [ Mon Jan 16, 2012 1:53 pm ]
Post subject:  IUPAC naming and partial charge problems on 3D

The lignad naming is wrong beyond recognintion. It seems that there is some odd shift with partial charges also on the 3D-models. Please check some of my ligands (patenttiligandit) to see the problem. Also, why I cannot dock directly the sdf file? It would be so much easier to use the file directly and then download a single file containing the relevant results rahter than individually selecting one ligand at a time for docking...

Author:  bikadi [ Mon Jan 16, 2012 6:43 pm ]
Post subject:  Re: IUPAC naming and partial charge problems on 3D

IUPAC naming is a third-party software, we are well aware that it is in an experimental stage. I was unable to find a ligand called patenttiligandit in your account. Could you please put a link to your ligand? Of course partial charge calculation methods greatly influence the calculated charges, e.g PM6 calculates much higher absolute values than the other methods, however, the docking calculation is parametrized to handle this problem.
You can select multiple ligands for docking by selecting the relevant checkboxes. It is still true that ligands are treated independently in later phases. Our new product in development can handle this issue better. If you are interested, you can try out the beta version for free at: http://user.althotas.com.

Zsolt

Author:  vittuperkele [ Mon Jan 16, 2012 6:58 pm ]
Post subject:  Re: IUPAC naming and partial charge problems on 3D

Here's straight link for such ligand with wrong iupac nomenclature http://www.dockingserver.com/web/dockin ... ds/107785/
I gotta try the beta-version, thank you for the info (and superb, high quality and cost effective service!)

Author:  bikadi [ Mon Jan 16, 2012 7:28 pm ]
Post subject:  Re: IUPAC naming and partial charge problems on 3D

I thougth that the charges are calculated by PM6 when you mentioned strange values :) Your result is typical for PM6, it is fine, carbons are often calculated to be "supercharged", when halogens are attached to it. When the docking calculations start, Dockingserver select the appropriate parameters based on the applied charge calculation method, so you do not have to worry about that. And thank you for your kind words!

Author:  vittuperkele [ Mon Jan 16, 2012 8:58 pm ]
Post subject:  Re: IUPAC naming and partial charge problems on 3D

I seem to have problems when expressing myself ;) .. But yes - indeed, the calculations seem to be okay - just the IUPAC naming was the problem :)

Author:  hazaie [ Thu Feb 09, 2012 1:49 pm ]
Post subject:  Re: IUPAC naming and partial charge problems on 3D

The IUPAC naming function has been implemented to DS.
Please be aware that the function can be used with prepared ligands only.
Happy Docking :)

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