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#1 2026-04-09 07:54:56
- ThCu
- Member
- Registered: 2026-04-09
- Posts: 2
Intramolecular sobEDA analysis
Hi Prof. Lu, hi everyone,
I just have a question regarding the possibility to conduct an intramolecular sobEDA analysis. I am uncertain how to generate the fragment input file required for the sobEDA script, as after breaking the bond I want to study, there is still only one fragment. Am I able to generate input files for the sobEDA method for intramolecular systems? Any advice would be highly appreciated.
Thank you in advance.
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#2 2026-04-09 19:10:01
Re: Intramolecular sobEDA analysis
To realize this aim, the whole molecule must be dissected as two fragments, just like a dimer. You need to properly remove atoms around the bond to be dissected, and some hydrogens usually need to be properly added to saturate the dangling bonds. Sometimes the conformation of the two fragments should be adjusted to avoid occurrence of artificial steric effect between the two fragments.
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#3 2026-04-10 06:50:34
- ThCu
- Member
- Registered: 2026-04-09
- Posts: 2
Re: Intramolecular sobEDA analysis
Thank you for the quick reply. I think I know what you mean. Just one concern: Wouldn't altering the structure on such a level falsify the results to some extend? Anyway, I will give it a try. Thank you again.
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#4 2026-04-10 22:21:22
Re: Intramolecular sobEDA analysis
This will more or less introduce some artificial factors; however, by properly constructing the model dimer system, the artifical effect can be minimzed to a negligible extent. For example, one may need to perform constraint optimization to avoid occurrence of evident steric repulsion between the two fragments in the originally bonded region...
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