Re: [AMBER] : Membrane Dynamics

From: Albert <>
Date: Wed, 21 Dec 2011 01:29:24 +0100

GPCR simulation is a very hot topic nowadays. It is worth Amber
developer to do something towards this purpose.

  I strongly suggest that the developer can consider the membrane system
builder, lipids forcefiled, relaxation protocol, ligand topology tools
during development. At least, cooperating with Desmond is also a good
choice since the system builder, lipids forcefiled and relaxation
protocol is good in Desmond. The only stuff is ligand topology and Amber
got such kind of tools to complement it.

On 12/21/2011 01:07 AM, Aron Broom wrote:
> Yes, there is no reason why you can't do a simulation with a protein in a
> membrane in AMBER. I'm not aware of any tutorials on this topic, but there
> are some web services where you can get the coordinate files for
> pre-equilibrated membranes, this might be a good place to start.
> On Tue, Dec 20, 2011 at 7:03 PM, Carlos Simmerling<
>> wrote:
>> I'm not sure it's that simple- in principle, Amber can do membrane
>> simulations and examples have been published. If one is thinking of a
>> particular simulation method that is wanted to enforce aspects of membrane
>> structure and perhaps stop the inaccurate force fields from doing bad
>> things, then it's a different question than just whether Amber can actually
>> run membrane simulations...
>> On Tue, Dec 20, 2011 at 6:54 PM, Albert<> wrote:
>>> As far as I know, Amber doesn't support membrane protein simulation. It
>>> is said that the next version of Amber may update this function.
>>> On 12/20/2011 04:56 PM, Rajesh Singh wrote:
>>>> Dear All,
>>>> I am facing problems in performing MD of membrane proteins (GPCRs). I
>>> would
>>>> highly appreciate if anybody can provide me a tutorial for performing
>>>> membrane dynamics using AMBER.
>>>> Thanks and regards
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Received on Tue Dec 20 2011 - 16:30:05 PST
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