Free Programs, Molecular Coordinates, & Files

Below is a list of free files to download. Please reference our lab if you use these in any public form, i.e., publications or presentations.

Programs

Model Membranes (CHARMM36-based coordinates)

E. coli cytoplasmic membrane (6-lipid types at 303.15K from BBA 2012): PDB, CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD
POPE/POPG (5.3:1 headgroup ratio) simple model of E. coli (303.15K from BBA 2012): PDB, CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD
Chlamydia Membrane model for Elementary Body (9-lipid types at 303.15K from BBA 2011): PDB, CHARMM PSF, and X-Plor/NAMD PSF
Chlamydia Membrane model for Reticular Body (9-lipid types at 303.15K from BBA 2011): PDB, CHARMM PSF, and X-Plor/NAMD PSF

CHARMM36 FF (Note: If you run these simulations in NAMD you MUST use NAMD 2.7b3 or newer versions with vdwForceSwitching turned on)

DPPC Bilayer (323.15K, NPT, 40ns, 72 lipids): PDB, CHARMM PSF, and CHARMM CRD
DMPC Bilayer (303.00K, NPT, 40ns, 72 lipids): PDB, CHARMM PSF, and CHARMM CRD
DOPC Bilayer (303.00K, NPT, 35ns, 72 lipids): PDB, CHARMM PSF, and CHARMM CRD
POPC Bilayer (303.00K, NPT, 35ns, 72 lipids): PDB, CHARMM PSF, and CHARMM CRD
POPE Bilayer (310.15K, NPT, 40ns, 80 lipids): PDB, CHARMM PSF, and CHARMM CRD

CHARMM27r FF

DPPC Bilayer (323.15K, A=64 Â/lipid, 50ns, 72 lipids): PDB, CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD
DPPC Bilayer (323.15K, A=64 Â/lipid, 50ns, 288 lipids): CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD
DMPC Bilayer (303.15K, A=60.7 Â/lipid, 50ns, 72 lipids): PDB, CHARMM PSF, and CHARMM CRD
POPE Bilayer (310.15K, A=65.2 Â/lipid, 10ns, 340 lipids, noLRCs): CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD
DPPC Monolayer (323.15K, A=64 Â/lipid, 25ns, 80 lipids): PDB, CHARMM PSF, and CHARMM CRD

CHARMM36 (Most up-to-date version of the CHARMM lipid FF): Prof. MacKerell website
CHARMM36-bacterial (cyclic chain for E. coli membranes & branched lipids): Stream/Notes files
CHARMM36-Cholesterol (update to cholesterol FF): Stream/Notes files
CHARMM27r (C27r, revised C27 for aliphatic chain of lipids): Par/Top files
CHARMM27rn (C27rn, force field for nitro compounds): Par/Top files
AMBER99 for use in CHARMM: Par/Top files (NOTE: CHARMM needs to be compiled with the AMBER keyword in the pref.dat file to be consistent with AMBER conversion factors)
AMBER99SB for use in CHARMM (Hornak, V., et al. Proteins: S.F.B. 65:712 (2006)): Par/Top files (NOTE: CHARMM needs to be compiled with the AMBER keyword in the pref.dat file to be consistent with AMBER conversion factors)
AMBER99-bs0 for use in CHARMM (Perez, A. et al. BJ. 92: 3817 (2007)): Par/Top files (NOTE: CHARMM needs to be compiled with the AMBER keyword in the pref.dat file to be consistent with AMBER conversion factors)