[Chimera-users] Lipid bilayer

Eric Pettersen pett at cgl.ucsf.edu
Fri Oct 12 14:40:09 PDT 2007

Hi Francesco,
	I'm not a VMD/Amber expert, so if anyone else on the list is then  
feel free to chime in.  I imagine that VMD will be able to output PDB  
format and possibly psf/dcd.  Normally PDB would be the "lingua  
franca" for these tools, but when you have a big lipid bilayer --  
which you won't find in any standard PDB file -- then there may be  
compatibility problems between the tools.  At any rate, I think you'd  
use VMD to create the molecule + bilayer, ship that over to Amber and  
so whatever simulation you are going to with it, then take that and  
use it in Chimera/Dock -- possibly stripped of the bilayer at that  
	Another stumbling block is getting Amber parameters for the lipids.   
You probably need to ask on the Amber list about that, but I think  
using the GAFF forcefield comes into play.


On Oct 11, 2007, at 10:21 PM, Francesco Pietra wrote:

> Eric:
> Is a lipid bilayer built with VMD (which is also installed on my  
> desktop, while
> NAMD is not on my parallel machine) transferable to the Amber-Dock- 
> Chimera
> world? This question because I am interested in very complicated - non
> polymeric - ligands and deeply modified peptides and proteins. I tried
> WMD-Paratool: much too time consuming, if at all workable at this  
> stage for my
> purposes. I found Antechamber a reasonable solution in this semi- 
> qualitative
> world.
> Though, I am open to keep my tools up-to-date.
> Thanks
> francesco
> --- Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>> Also, these posts to the Amber mailing list have some pertinent
>> references:
>> http://structbio.vanderbilt.edu/archives/amber-archive/2007/3900.php
>> http://structbio.vanderbilt.edu/archives/amber-archive/2007/3901.php
>> --Eric
>> 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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