Re: [AMBER] Thermodynamic integration for protein-protein interactions

From: <>
Date: Sat, 20 Feb 2021 00:02:29 +0800

   how about using MMPBSA method to evaluate the effect of mutation on protein
   binding? Iâm not sure.


   On 02/19/2021 23:33, [1]David A Case wrote:

     On Fri, Feb 19, 2021, WW wrote:
>I would like to investigate how point mutations in one protein affect the
>binding affinity of protein-protein interaction using Amber18. Running
>Amber-TI module as-is results in an error saying that the maximum number
>softcore atoms is 200.
     I'm not sure what sort of calculation you are thinking about here. I'd
     suggest making the softcore region be the amino acid that is mutating.
     perform the mutation once in the presence of the second protein, then
     in its absence. The difference will give you an estimate of the effect of
     the mutation on protein-protein binding. There is no need for any large
     softcore region, which you almost certainly do not want.
     ....good luck....dac
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Received on Fri Feb 19 2021 - 08:30:02 PST
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