Dear Carlos,
Great to see these studies. For the IDP work, could you send me the Amber configuration scripts used for minimization, equilibration and production runs for TI? I would like to learn how to set up the system. An example PDB will be great.
For my compiled Amber18, I did not see the pmemdGTI program, is it compiled with specific parameters? I only see pmemd.cuda.
Thanks,
Best,
Zizhang
> On Mar 22, 2021, at 3:58 PM, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> we've done calculations on protein-protein binding affinity for sets of
> mutations using Amber pmemd TI on GPUs and found (in most cases) very good
> accuracy vs experiment:
>
> Dissecting the Energetics of Intrinsically Disordered Proteins via a Hybrid
> Experimental and Computational Approach. Zou, J., Simmerling, C., Raleigh,
> D., The Journal of Physical Chemistry B 123 (49), 10394-10402 2019
> https://pubs.acs.org/doi/10.1021/acs.jpcb.9b08323
>
> we also have a recent review that discusses accuracy of calculations, with
> references to recent examples
>
> Protein storytelling through physics
> Emiliano Brini, Carlos Simmerling, Ken Dill
> https://science.sciencemag.org/content/370/6520/eaaz3041
>
>
>
> On Mon, Mar 22, 2021 at 2:01 PM zz sheng <shengzizhang.gmail.com> wrote:
>
>> Hi All,
>>
>> I would like to estimate protein mutations on protein-protein interaction
>> affinity using thermodynamics integration algorithm in pmemd. Does anyone
>> tested the accuracy of the approach and how to setup MD simulations in
>> Amber?
>>
>> Thanks,
>>
>>
>> Best,
>>
>> Zizhang
>>
>>
>>
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Received on Thu Mar 25 2021 - 07:30:02 PDT
