Hi Michal,
I dont think there is a rigorous simple answer to this, calculating formal
charges normally needs bond orders and getting bond orders from geometry is
not 100% reliable. There is a blog post on how to do that in rdkit here:
https://greglandrum.github.io/rdkit-blog/posts/2022-12-18-introducing-rdDetermineBonds.html
Since you mention "from formula sum", there are chemically reasonable
molecule sum formulas that could be both a cation or anion. I really hope I
didnt miscount hydrogens, but consider C4H8NO2, which could be
NH3+-CH2-CH=CH-COOH or NH2-(CH2)3-COO-
Kind Regards,
Thomas
On Sun, Nov 10, 2024 at 6:37 PM Husak Michal via AMBER <amber.ambermd.org>
wrote:
> **Warning** The sender address (Husak Michal via AMBER ) can not be
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> proceed.
> Hi
>
> We develop a method for fast molecular crystal structure verification
> based on GAFF2 force field usage ...
> The isdue is detection of anions an kations ...
> From my understanding antechamber must have -nc 1 for kation an - nc -1
> for anion.
> But is there any way how to detect the charge of the fragments from its 3D
> coordinates or formula sum automaticaly ?
> I can not find any simple method ....
>
> Michal Husak
> UCT Prague ...
>
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*Dr. Thomas Steinbrecher*
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Received on Mon Nov 11 2024 - 00:00:02 PST
