[AMBER] Thermodynamic integration for protein-protein interactions

From: WW <wanlei1991.gmail.com>
Date: Fri, 19 Feb 2021 09:35:25 -0500

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?

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Received on Fri Feb 19 2021 - 07:00:02 PST
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