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@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@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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