[Chimera-users] Lipid bilayer

[Eric Pettersen]

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  
point.
	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.

--Eric

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
>>>>
>>>>
>>>>
>>>> ___________________________________________________________________ 
>>>> __
>>>> _
>>>> ______________
>>>> Be a better Heartthrob. Get better relationship answers from
>>>> someone who knows. Yahoo! Answers - Check it out.
>>>> http://answers.yahoo.com/dir/?link=list&sid=396545433
>>>> _______________________________________________
>>>> Chimera-users mailing list
>>>> Chimera-users at cgl.ucsf.edu
>>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>>
>
>
>
>        
> ______________________________________________________________________ 
> ______________
> Fussy? Opinionated? Impossible to please? Perfect.  Join Yahoo!'s  
> user panel and lay it on us. http://surveylink.yahoo.com/gmrs/ 
> yahoo_panel_invite.asp?a=7
>