[AMBER] Handling new atom types - bonded

From: Sam Walsworth (Researcher) <"Sam>
Date: Thu, 23 Dec 2021 15:49:58 +0000


I've noticed that leap gives me "Incorporating Non-Bonded adjustments." when I try to saveamberparm on one of my organosilver complexes, and that the .gro file I get from ParmEd shows my silver atom non-bonded despite providing bond and angle parameters for those containing silver (and .mol2 file having the correct connectivity etc).

My question is if there is a default way to handle new atoms bonded and/or non-bonded, or does this largely depend on the nature of the atom? The final hurdle for me is somehow convincing leap that the silver atoms present aren't supposed to be non-bonded.

Thank you in advance
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Received on Thu Dec 23 2021 - 08:00:02 PST
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