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

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Fri, 17 May 2019 18:18:09 +0000

Hi,
Thank you for clearing the doubt.
any ideas on how to analyse the outputs generated after putting in these paramters "mcwat=1, ! Turns on MCWAT
mcresstr='WAT ', ! Defines residue for exchanging
nmc=1000, ! Number of monte carlo steps to run
nmd=1000, ! Number of molecular dynamics to run before monte carlo steps run"



________________________________
From: Charles Lin <Charles.lin.silicontx.com>
Sent: Friday, May 17, 2019 7:45 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Simulating Water Exchange to Buried Binding Sites

So the current implementation only allows exchanges of the same type of residue. There's a string that sets what type of residue is being exchanged (Mcresstr), we could definitely add it so you could do multiple different types of solvent molecules. So say water and methanol could freely be exchanged.

In terms of how to use the program, you define your variables and the exchange rates.

mcwat=1, ! Turns on MCWAT
mcresstr='WAT ', ! Defines residue for exchanging
nmc=1000, ! Number of monte carlo steps to run
nmd=1000, ! Number of molecular dynamics to run before monte carlo steps run

There's a variables that can be used to set a smaller subsystem box, so you're not exchanging in the entire simulation box (mcboxshift).

-Charlie

´╗┐On 5/17/19, 10:15 AM, "Matias Machado" <mmachado.pasteur.edu.uy> wrote:

    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. [https://doi.org/10.1016/j.str.2015.05.006] have been developed, still such approach may not be suitable for all systems.

    Best,

    Matias

    ------------------------------------
    PhD.
    Researcher at Biomolecular Simulations Lab.
    Institut Pasteur de Montevideo | Uruguay
    [pasteur.uy/en/labs/biomolecular-simulations-laboratory/]
    [http://www.sirahff.com]

    ----- Mensaje original -----
    De: "Debarati DasGupta" <debarati_dasgupta.hotmail.com>
    Para: amber.ambermd.org
    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?

    Thanks
    Regards



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Received on Fri May 17 2019 - 11:30:03 PDT
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