Re: AMBER: lipid bilayer

From: Vlad Cojocaru <>
Date: Thu, 11 Oct 2007 14:09:23 +0200

Dear Santanu,

Amber does not provide lipid parameters with the distribution ... So.
first you might want to take a look at this paper

Jojart B and Martinek T, 2007, J. Comput. Chem. 28:2051-2058

Leap is not capable of building lipid bilayers. You might want to build
your membrane with VMD but then you should read the relevant literature
and properly equilibrate your membrane (NAMD has more options for
pressure control than AMBER which may be very relevant especially during
equilibration)... You may also use one of the available pre-equilibrated
membranes and adapt it to the parameters you use ...

Unfortunately, there are very few studies that I am aware of with MD of
membranes or membrane-protein complexes done in AMBER. Even with
parameters that are compatible with the amber ff (as in the paper above)
you would probably want to use NAMD for running your simulations....

After you have an equilibrated membrane, the second step wil be to place
your protein in the membrane... You need to search for available
literature onmethods how to do that...

A few papers which you might find interesting:

Berkowitz ML et al, Chem Rev 2006, 1527-1539
Kandt C et al, Methods 2007, 41:475-488
Gullingsrud and Schulten, Biophys. J. 2004, 86: 3496-3509

Hope this helps

san_amber roy wrote:

> Dear amber users,
> I want to add lipid bilayer to a protein.
> Is it possible to do it using "leap" program? Please kindly say few
> words regarding this.
> Thanks,
> Santanu

Dr. Vlad Cojocaru
EML Research gGmbH
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69118 Heidelberg
Tel: ++49-6221-533266
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EML Research gGmbH
Amtgericht Mannheim / HRB 337446
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Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
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Received on Sun Oct 14 2007 - 06:07:23 PDT
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