Re: [AMBER] Simulating Water Exchange to Buried Binding Sites

From: Matias Machado <>
Date: Fri, 17 May 2019 11:14:06 -0300 (UYT)

I'm adding a follow up question...

Is this new feature implemented on AMABER in a general way so that other solvent molecules than atomistic water can be exchanged with the solvent?

I'm asking this because solvation is a big issue when building and equilibrating big and complex systems like viral particles or membrane proteins (to mention a few). This issue is even magnified in case of coarse-grained models, which granularity prevents for the correct initial solvation, but are needed for overcoming the computational demand. In this regard, some alternative strategies like self-protein/membrane assemble by Samson et al. [] have been developed, still such approach may not be suitable for all systems.



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Debarati DasGupta" <>
Enviados: Jueves, 16 de Mayo 2019 10:21:44
Asunto: [AMBER] Simulating Water Exchange to Buried Binding Sites

Hi Amber users,
Can anyone tell me whether there is any tutorial or any information on how to implement this recent work published in JCTC.
Has anyone used the methodology described in the above publication?


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Received on Fri May 17 2019 - 07:30:02 PDT
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