Re: Creating a New Patch for RNA

From: Josh Vermaas (
Date: Mon Sep 05 2022 - 05:39:14 CDT

Hi Colin,

That basically sounds similar to what I would have done. In the grand
scheme of things, adjusting 1 charge by -0.003 is peanuts. That being
said, its connected to a phosphate group, so a useful experiment is to
see what the charge distribution on a phosphorylated imidazolium would
look like. You have the freedom to put the charge wherever you like, and
CGenFF may have decided that there is a small amount of charge transfer
to the phosphate. So if you compare the charges for the RNA piece
obtained from CGenFF with the regular nucleic acid force field, it may
be that the only charge change occurs on the phosphate group, rather
than on the carbon.


On 9/4/22 18:04, Collin Nisler wrote:
> 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.
> CollinĀ 

This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST