[Chimera-users] Lipid bilayer

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 11 09:35:04 PDT 2007

Hi Francesco,
I would not recommend trying to build a lipid bilayer in Chimera.  I  
do not have specific information, but I would first look for such  
tools in simulation programs such as Amber.  You can also look for  
publications where simulations in lipid bilayers were performed.  If  
there are examples you think are well done, you can try to follow the  
protocol described in the paper.

I thought there might be coordinates available for an equilibrated  
bilayer, but was not able to find it with a little searching.  You  
might be able to find such a thing with more careful searching.   
Another suggestion is to post your question on the amber mailing list  
(see http://amber.scripps.edu/#reflector ) or the computational  
chemistry mailing list (see ccl.net ) or even search their archives.


p.s. about your other question on "cleaning up" structures, if you  
mean deleting extra things you don't want, you can use Chimera's  
"delete" command, or select the unwanted things and then use  
"Actions... Atoms/Bonds... delete"
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 11, 2007, at 7:38 AM, Francesco Pietra wrote:

> How far (and how close to reality) can we go in building a lipid  
> bilayer with
> Chimera for use with Amber and Dock? If possible, where to drop in  
> Chimera?
> I mean a lipid bilayer for a model of ion channel, i.e. ca 30A thick.
> Thanks
> francesco pietra
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