Hi Ren,
> Is there any general protocol to do the initial minimization and relax, as well as produce modeling for a membrane protein system?
Membrane-bound protein systems are still fairly cutting edge in Amber. There are some common features of protocols for membrane-bound proteins embedded in a bilayer system. After an initial minimization, most methods proceed by very slowly heating the system. I've seen publications that use some type of restraint on the lipid bilayer and membrane-bound proteins during portions of the heating as well. In order to reproduce some experimental values such as area per lipid, electron density profiles, diffusion coefficients, and tail order parameters, it is necessary to use a barostat as well.
I'd like to point out one issue that we are aware of in "An Amber Lipid Force Field Tutorial". Using a CHARMM-GUI structure as a starting point can cause one issue in LEaP. LEaP's "setBox" causes LEaP to overestimate the periodic box size of the system, because the lipids "stick out" of the sides of the structure. As a result of this, in the beginning of your production for the lipid bilayer (with a membrane-bound protein), the periodic box dimensions rapidly decrease. If you're not familiar with Amber or lipid simulations, I would approach this extremely carefully. A box size can be manually set with the command:
set unit box { xdim ydim xdim }
We are working on automating a way to set the box size to address this issue so that initial decrease in periodic box boundaries is not an issue.
> Could anyone provide some articles using amber as tool to do membrane protein modeling?
There are several options for lipid simulations in Amber: Initially, there were attempts to use the GAFF parameters as well as some lipids available in the Glycam force field. Now, the Lipid11 and GAFFlipid force field have been available for Amber. In addition, several Amber developers have been working on the next logical steps for lipid force fields in Amber.
> Despite of energy items and rmsd of protein, what other parameters, especially those parameters related to lipid bilayer should be monitored during the simulation?
During the simulation, the area per lipid of the bilayer will certainly be impacted by the presence of a protein. It is possible through various scripts to calculate the area per lipid of a membrane-bound protein system by taking into account the area of the membrane-bound protein. In addition, it is still possible to examine diffusion rates, electron densities, and tail order parameters.
All the best,
Ben Madej
Walker Molecular Dynamics Lab
On Mar 24, 2013, at 4:55 PM, "Kong, Ren" <rkong.tmhs.org>
wrote:
> Dear all,
>
> I notice that Amber 12 include a new force field lipid 11 for membrane protein modeling.
> I want to do modeling for a membrane system. I have got through the tutorial on the amber website but I still have some questions.
>
> Is there any general protocol to do the initial minimization and relax, as well as produce modeling for a membrane protein system?
> Could anyone provide some articles using amber as tool to do membrane protein modeling?
> Despite of energy items and rmsd of protein, what other parameters, especially those parameters related to lipid bilayer should be monitored during the simulation?
>
> Thanks a lot.
>
> Best,
> Ren
>
>
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Received on Sun Mar 24 2013 - 22:30:02 PDT
