Thank you for the helpful suggestions. One additional question I had was
that is there a tool within AMBER to look at methylation of RNA?
Please advise.
Thank you.
PN
On Thu, Dec 8, 2022 at 8:40 AM David A Case <david.case.rutgers.edu> wrote:
> On Wed, Dec 07, 2022, Prithviraj Nandigrami via AMBER wrote:
>
> >The pdb file I used is taken directly from rcsb.org (crystal structure).
>
> It would be of help to know the PDB ID here. But it looks like you have
> several problems:
>
> 1. the 5' nucleotide has a phosphate group attached, which is not present
> in
> the Amber library for a 5' residue. This leads to the "created a new atom"
> messages, which will eventually be fatal. Amber has a
> "terminal_monophosphate.lib" file that you can load that should solve this
> problem -- but you might also want to just remove the initial OP1,OP2 and P
> atoms instead. The structure in the PDB file is chemically unreasonable,
> and you might want to think about what molecule you really want to
> simulate.
>
> 2. Most of the atoms in residue 55 are missing in the input PDB file.
> LEaP
> will try to add these, but it is not very smart about how it does that.
> You
> might want to get a better starting model using some other software.
>
> 3.
> >Warning: There is a bond of 6.895 angstroms between O3' and P atoms:
> >------- .R<G 61>.A<O3' 34> and .R<G 62>.A<P 1>
>
> You need to check visually about what is really going on here. Are
> residues
> 34 and 62 really in different chains? Then you would need to add a TER
> card
> between them to prevent Amber from trying to create a bond.
>
> ....hope this helps.....dac
>
>
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Received on Fri Dec 09 2022 - 15:00:03 PST
