Re: [AMBER] : Membrane Dynamics

From: Vlad Cojocaru <>
Date: Wed, 21 Dec 2011 07:37:27 +0100

Dear Albert,

If you follow previous threads regarding lipid simulations with Amber ff, you'll realize that some studies are done with the Gaff parameters available in the literature

However, as the gaff parameters have the problem of getting a gel-phase bilayer in pure npt sim, you'd need to run the simulations with namd and apply a surface tension.

Alternatively, you can use glycam for lipids as well. However same problem as with gaff and besides glycam uses a different 1-4 scaling factor than amber, so another level of complication.

To my knowledge, the only atomistic force field for lipids that reproduces nicely lipid properties in pure npt sims is the newest charmm ff.

The gaff parameters need some attention for further development to achieve stable npt simulations with lipids

Dr. Vlad Cojocaru
MPI Muenster
Roentgenstrasse 20
48149 Muenster
Tel: +49-251-70365324
*** Sent from my Sony XPERIA ARC
*** Sorry for being short
*** Sorry for any errors
Albert <> wrote:
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
>>> AMBER mailing list
>> AMBER mailing list
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Received on Tue Dec 20 2011 - 23:00:02 PST
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