Nice!... I'll give it a try...
By the way, keyword "mcresstr" isn't defined in the new AMBER Tools 19 manual.
Are you planning on implementing a more sophisticated way of defining the exchange region instead of equally padding the box boundaries by mcboxshift relative to the box centre? e.g. according to a residue selection and a cut-off radius, that could be very helpful in intricate molecular systems.
Best,
Matías
----- Mensaje original -----
De: "Charles Lin" <Charles.lin.silicontx.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Viernes, 17 de Mayo 2019 14:45:25
Asunto: 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator.
This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 17 2019 - 11:30:03 PDT
