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On this page I provide several molecular configurations and force field files that may make life easier for some simulators (especially those interested in biomembranes). Note that all images and downloadable files here are copyrighted by me, David Bostick (01/10/2007). Please use them at your own risk and with proper acknowledgment of my web site and of their associated publications. Some (though not all) of the items provided in this web publication were products of National Science Foundation (NSF) funding, and thus, the following disclaimer applies: Any opinions, findings, and conclusions or recommendations expressed in this (web) publication are those of the author (me, David Bostick) and do not necessarily reflect the views of the NSF. |
| Description | Picture | Reference | Coordinates | Force Field Files |
|---|---|---|---|---|
| AmtB Channel in POPC bilayer. 117276 particles. Equilibrated at 298 K & 1 atm. |  |
PLoS Comp. Biol. 2007. 3(2): 0231-0246 | pdb file | Gromacs Format - tarzip bundle |
| AmtB Channel Monomer with Ammonium in the Am1 binding site. Site and structure were determined by umbrella simulations. |  |
PLoS Comp. Biol. 2007. 3(2): 0231-0246 | pdb file | — |
| AmtB Channel Monomer with Ammonium in the Am5 binding site. Site and structure were determined by umbrella simulations. | |
PLoS Comp. Biol. 2007. 3(2): 0231-0246 | pdb file | — |
| § OPLS United Atom force field for lipids. These were derived in the Berkowitz lab at UNC-Chapel Hill. So far I only have DPPC and POPC, but these are nice choices for membrane protein systems. The force field behaves nicely (in principle and practice) with the OPLS all atom force field for proteins. | — | § J. Comp. Chem. 1999. 20: 531-545 | — | § Gromacs Format - tarzip bundle |
| Small POPC bilayer (50 lipids). Decently equilibrated (298 K & 1 atm). Great for building larger bilayers! 12563 particles. |  Generic Bilayer |
— | pdb file | see § above |
| Medium POPC bilayer (200 lipids). Decently equilibrated (298 K & 1 atm). 50252 particles. | Generic Bilayer |
— | pdb file | see § above |
| Large POPC bilayer (450 lipids). Decently equilibrated (298 K & 1 atm). 113037 particles. | Generic Bilayer |
— | pdb file | see § above |
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