Re: [AMBER] tleap does not recognize inosine

From: David A Case <>
Date: Tue, 20 Jul 2021 11:10:56 -0400

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.


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Received on Tue Jul 20 2021 - 08:30:02 PDT
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