we recently published work using Amber TI that included calculation of the
impact of mutations on protein-protein binding affinities, for complexes
involving stable proteins and for IDPs. The methods described there may be
helpful for your work.
Dissecting the Energetics of Intrinsically Disordered Proteins via a Hybrid
Experimental and Computational Approach
<
https://doi.org/10.1021/acs.jpcb.9b08323>. Zou, J., Simmerling, C.,
Raleigh, D., The Journal of Physical Chemistry B 123 (49), 10394-10402 2019
DOI: 10.1021/acs.jpcb.9b08323
On Fri, Feb 19, 2021 at 9:36 AM WW <wanlei1991.gmail.com> wrote:
> Hi all,
>
> 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 of
> softcore atoms is 200. Looking through the mailing list, I saw that I could
> change that limit by modifying the file: "cuda/gti_simulationConst.h" so
> that I have a higher limit:
>
> MaxNumberTIAtom = 4000
> MaxNumberTIPair = 2000
> GPUPotEnergyTerms = 800
> GPUKinEnergyTerms = 200
>
>
> However, this results in a different error:
>
> Error in `pmemd.cuda_DPFP': double free or corruption.
>
> Is this coming from a lack of available memory? I was just wondering
> whether it is possible to do Amber-TI on P-P interactions through
> modifications of the existing code?
>
> Thanks!
> Wanlei
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Feb 19 2021 - 08:00:02 PST
