Coordinates


Lipid Coordinate Sets




Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites Joseph W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor. J. Phys. Chem. B, 114, 7830-7843 (2010).


Table 1. Coordinate set collections: 20 coordinate sets spaced 1 ns apart, from the final 20 ns of each lipid bilayer NPT simulation.

System File Format
DLPC CHARMM :: PDB
DMPC CHARMM :: PDB
DPPC CHARMM :: PDB
POPC CHARMM :: PDB
POPC CHARMM :: PDB




Coordinate Sets from Older Publications, in both CHARMM and PDB Formats

A Molecular Dynamics Study of the Response of Lipid Bilayers and Monolayers to Trehalose. Anna Skibinsky, Richard M. Venable and Richard W. Pastor, Biophysical Journal, 89, 4111-4121 (2005).

Table 2. Final coordinate sets from NPAT (constant area) bilayer simulations, identified via the area/lipid, A

System A = 54 A = 64 A = 80
DPPC + Water CHARMM :: PDB CHARMM :: PDB CHARMM :: PDB
Trehalose + DPCC + Water CHARMM :: PDB CHARMM :: PDB CHARMM :: PDB
All NPAT bilayer coordinate sets in one archive file.

Table 3. Final coordinate sets from NVT (constant area, height) monolayer simulations, identified via the area/lipid, A

System A = 54 A = 64 A = 80
DPPC + Water CHARMM :: PDB CHARMM :: PDB CHARMM :: PDB
Trehalose + DPCC + Water CHARMM :: PDB CHARMM :: PDB CHARMM :: PDB
All NVT monolayer coordinate sets in one archive file.

Constant Surface Tension Molecular Dynamics Simulations of Lipid Bilayers with Trehalose, Richard M. Venable, Anna Skibinsky, and Richard W. Pastor, Molecular Simulation, 32, 849-855 (2006).

Table 4. Final coordinate sets from NPγT (constant applied γ) bilayer simulations, identified via the applied surface tension (γ) system

System γ = 10 γ = 17 γ = 25
DPPC + Water CHARMM :: PDB CHARMM :: PDB CHARMM :: PDB
Trehalose + DPCC + Water CHARMM :: PDB CHARMM :: PDB CHARMM :: PDB
All NPγT bilayer coordinate sets in one archive file.

The above two published lipid and trehalose studies utilized custom pre-combined topology and parameter files, available in this archive file. An example of how to make a CHARMM PSF for any of these systems can be found here. Simply omit the initial sugar part for the DPPC + water only systems.

UPDATE: A new carbohydrate force field is now available, and a new lipid force field is pending; after its release, pre-combined topology and parameter files, along with a new PSF example will be provided.



These external web sites have lipid coordinates posted by former group or lab members, and feature data from publications involving current group members. The C27r parameters represent a substantial improvement in the alkane chain dihedral term.

More recent CHARMM C27r parameter based coordinate sets, from the lab of Dr. Jeff Klauda at the Univ. of Maryland.
Earlier CHARMM C27 parameter based coordinate sets, from the lab of Dr. Scott Feller at Wabash College.