Re: [rDock-list-def] Failure to handle charges in ligands

[Tim D. <tdu...@gm...>]

Ah, thanks. That's good to know.
I'm using RDKit that adds the info as CHG lines and not to the atom lines
as that is the "correct" way to do it now.
Tim

On Thu, Oct 8, 2020 at 6:11 PM Markus Metz <me...@gm...> wrote:

> Hi Tim:
> I know you did not ask this.
> But for reference:
> If you use for example openbabel the column charges are added and all
> works fine.
> Markus
>
>
> On Oct 8, 2020, at 9:33 AM, Tim Dudgeon <tdu...@gm...> wrote:
>
> This was raised a long time ago, but the problem seems to remain:
> https://sourceforge.net/p/rdock/mailman/message/34741112/
>
> rDock is not respecting the CHG lines in the molblock section.
> It reports out messages like:
> **WARNING** RBT_MODEL_ERROR at ../src/lib/RbtMdlFileSource.cxx, line 413
> N13 makes too many bonds
>
> The SDF it writes out is missing the charge information and so the
> molecule is not correct.
> Presumably, also, if the charges are missing then the energetics of the
> docking scoring must be badly wrong?
>
> Are there plans to address this?
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