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

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

Tim:
Please check out the rdkit user list.
Andrew Dahlke provided also a python script to overcome this issue.
best,
Markus

> On Oct 8, 2020, at 10:19 AM, Tim Dudgeon <tdu...@gm...> wrote:
> 
> 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... <mailto: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... <mailto: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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>