your log says this:
Created a new atom named: P within residue: .R<C5 1>
Created a new atom named: OP1 within residue: .R<C5 1>
Created a new atom named: OP2 within residue: .R<C5 1>
5' phosphate groups are not present in the residue template. there are a
few ways to deal with it. you can rename the residue for these three atoms
in your PDB to "OHE", or you could delete them.
there are lots of good discussions on this in the email reflector archive
which is searchable from the ambermd.org page.
for example, this one might be helpful for you:
http://archive.ambermd.org/201212/0315.html
On Sat, May 4, 2024 at 12:37 AM Kavinda Kashi Juliyan Gunasinghe via AMBER <
amber.ambermd.org> wrote:
> Dear Users,
>
> I have been trying to simulate a RNA molecule with the PDB ID: 2miy.
> However, when trying to parameterize it using OL3 force-field, I
> encountered an error which says three of the atoms do not have a type and
> therefore, gives 3 errors. However, when running PDB4AMBER it did not show
> any of these errors. How can I resolve this? I have attached the leap.log
> file and the PDB file for my RNA molecule.
>
> Thank you so much,
> Kind regards,
> Kavinda
>
>
>
>
>
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Received on Sat May 04 2024 - 08:30:02 PDT
