[Chimera-users] Lipid bilayer
chiendarret at yahoo.com
Thu Oct 11 22:21:16 PDT 2007
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
Though, I am open to keep my tools up-to-date.
--- Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 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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