Creating a New Patch for RNA

From: Collin Nisler (
Date: Sun Sep 04 2022 - 17:04:15 CDT

Hello all, I am attempting to create a patch for RNA by adding an imidazolium group to the 5' phosphate. I have the parameters for the new molecule generated from cgenff, and obviously for the RNA, but I'm struggling to figure out how to combine the two. I submitted the entire nucleotide with the imidazolium group to cgenff, but if I use the charges from this output starting at the 5' C (where the patch starts), they don't quite add up to -1. This result is obvious because the charges were provided in the context of the entire nucleotide, but I adjusted the charge of the 5'C by -.003 to get an even -1 charge for the patch. I then use the angle and bond parameters from cgenff, and I am able to run the system. I am not confident that this is a good way to do this, so I would appreciate any suggestions for how this can be done more rigorously, or whether this adjustment is fine. Thank you very much in advance.


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