Dear Thamires,
You need both an lib file and frcmod parameters. If it is standalone inosine as a nucleoside, you will need to make your own parameters.
For just the inosine base charges in a nucleotide:
I have ESP charges for inosine in RNA.
https://pubs.acs.org/doi/full/10.1021/ja9842565 <
https://pubs.acs.org/doi/full/10.1021/ja9842565>
As well, SantaLucia and Schlegel have RESP charges for the base,
all_modrna08.lib and all_modrna08.frcmod
https://pubs.acs.org/doi/abs/10.1021/ct600329w <
https://pubs.acs.org/doi/abs/10.1021/ct600329w>
Maria
> On Jul 20, 2021, at 11:10 AM, David A Case <dacase.chem.rutgers.edu> wrote:
>
> On Tue, Jul 20, 2021, Thamires Rocco Machado wrote:
>>
>> I'm studying a protein that has inosine as its substrate. I'm not getting
>> amber to recognize inosine when I load the PDB file into tleap. I
>> researched that amber has parameters for inosine,
>
> I don't know that inosine is in any standard library. You might look
> closely at the research you did, to find more details. Further, "inosine"
> as a protein substrate is probably chemically different from the nucleotide "inosine" that might be incorporated into a nucleic acid. (e.g. your pdb
> file looks like a nucleoside.
>
> It is likely that you can just feed your ligand to antechamber to get GAFF2
> parameters. It's also worth doing a search on "inosine Amber", if you've
> not already done that.
>
> Some one on the list might also chime in with some more detailed help.
>
> ....dac
>
>
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Received on Tue Jul 20 2021 - 09:00:03 PDT
