[Chimera-users] Lipid bilayer

Eric Pettersen pett at cgl.ucsf.edu
Thu Oct 11 10:37:09 PDT 2007

Also, these posts to the Amber mailing list have some pertinent  



On Oct 11, 2007, at 9:35 AM, Elaine Meng wrote:

> 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.
> Best,
> Elaine
> 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
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> 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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