Re: [AMBER] tleap does not recognize inosine

From: Maria Nagan <>
Date: Tue, 20 Jul 2021 11:51:30 -0400

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. <>

As well, SantaLucia and Schlegel have RESP charges for the base,
all_modrna08.lib and all_modrna08.frcmod <>

> On Jul 20, 2021, at 11:10 AM, David A Case <> 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
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