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

[Markus M. <me...@gm...>]

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/ <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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