PR2025 for covalent protein-ligand binding

[xupengpeng02]

Summary

1. No longer enforce Cl to be Cl-.
2. For "merge glycine" functionality, add the edge case: when the first fragment contains glycine, do not merge
3. fix a KeyError in fragmentation.py
4. add DFTB HMO file

[cstein]

Hi Peng,

I will adjust slightly, especially for the Cl- vs Cl case. I completely understand what you want to achieve. Problem is that it then breaks all simulations in solution where Cl- is used as a counter ion.

I will find a solution. Thanks for catching the bugs also :)

Best

Casper

[xupengpeng02]

Dear Casper, Sorry, I don’t know how I missed this email! Yes, I totally understand the situation here. I wonder if a distance cutoff would help resolve or mitigate the issue (Cl-C covalent bond length on average ~ 1.76 Angs). You may already have come up with a good solution, given that I only saw this email a month later… Best regards, Peng

…

On Aug 12, 2025, at 7:17 AM, Casper Steinmann ***@***.***> wrote: cstein left a comment (FragIt/fragit-main#39) <#39 (comment)> Hi Peng, I will adjust slightly, especially for the Cl- vs Cl case. I completely understand what you want to achieve. Problem is that it then breaks all simulations in solution where Cl- is used as a counter ion. I will find a solution. Thanks for catching the bugs also :) Best Casper — Reply to this email directly, view it on GitHub <#39 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFTXVL7JWSIVRMSX54FZIUD3NHLM3AVCNFSM6AAAAAB5W6DO7KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTCNZZGA4DAMZVHA>. You are receiving this because you authored the thread.