Hello!
Pseudouridine (PSU) parameters are available from the work of Lahiri
and collaborators:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8956458/ -- Supplementary file2
Hope that helps!
Rodrigo.
On Fri, Feb 9, 2024 at 12:09 PM Debarati DasGupta via AMBER
<amber.ambermd.org> wrote:
>
> Hello RNA experts and modelers, I am very new to the RNA forcefields and simulations and I am trying to set up some MD on a RNA structure which has 2 modified uracils in the sequence. I have loaded the leap ff files as instructed and I am trying to see if someone can help me in parametrizing this modified residue.
> is there a place/database I can look into for modified lib/frcmod files for modified bases in RNA?
> > source leaprc.gaff2
> > source leaprc.RNA.OL3
> > source leaprc.modrna08
> [cid:3cd96c5c-5b92-4ece-9181-55309560e2d5]
>
> The pdb is 6HMO. If someone can give a bit of guidance it will be much appreciated.
> Best,
> Debarati
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Received on Fri Feb 09 2024 - 12:30:03 PST
