Note1:
Cholesterol is built
using HyperChem and optimized using quantum calculations with Gaussian
03 at the Hartree-Fock level employing the 6-311G* basis set.
Cholesterol topology file is built using PRODRG web server.
Note2:
Topology files for DOPC,
DPPC, POPC, POPE are obtained from Biocomputing at the Calgary
University. These topology files need
lipid.itp file.
Note3:
Topology files for
DMTAP and POPG is obtained from Prof. Mikko Karttunen's group
(SoftSimu). His current address is Department of Chemistry, University
of waterloo.
Note1:
This is a new
GROMOS43a1-based force field for simulation of membranes with GROMACS
simulation package.
Note2:
Please make sure to cite
these articles if you use GROMOS43a1-S3 molecules.
1- Chiu S. W.
Vasudevan S. Jakobsson E. Mashl R. J. Scott H L, "Structure
of sphingomyelin bilayers: a simulation study",
Biophysical Journal,
2003, 85: 3624-3636
2- Pandit S. A. Vasudevan S. Chiu S. W. Mashl R. J. Jakobsson E. Scott H
L, "Sphingomyelin-cholesterol
domains in phospholipid membranes: atomistic simulation.Biophysical", Journal, 2004, 87: 1092-1100
3- Pandit S. A. Chiu S. W. Jakobsson E. Grama A. Scott H L, "Cholesterol
surrogates: a comparison of cholesterol and 16:0 ceramide in POPC
bilayers",Biophysical Journal, 2007, 92: 920-927
4- Pandit S. A.
Chiu S. W. Jakobsson E. Grama A. Scott H L, "Cholesterol
packing around lipids with saturated and unsaturated chains: a
simulation study", Langmuir, 2008, 24:
6858-6865
5- Chiu S. W.
Pandit S. A. Scott H L. Jakobsson E, "An
improved united atom force field for simulation of mixed lipid
bilayers", J Phys Chem B, 2009,
113: 2748-2763.
Note:
Atomic
charges of lipid molecules have been changed as reported by
Chandrasekhar et al to be optimized for membrane simulation due to Chiu
et al.
1-
Chandrasekhar I. Kastenholz M. Lins R. D. Oostenbrink C. Schuler L. D.
Tieleman D. P. van Gunsteren W. F, "A consistent potential energy
parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark
of the GROMOS96 45A3 force field", Eur Biophys J, 2003, 32: 67-77.
2- Chiu S. W.
Clark M. Balaji V. Subramaniam S. Scott H. L. Jakobsson E,
"Incorporation of surface tension into molecular dynamics simulation of
an interface: a fluid phase lipid bilayer membrane", Biophys J, 1995,
69:1230-45.
Note1:
These lipid
molecules can be used together with the AMBER99SB/AMBER99SB-ILDN/AMBER03
FF for proteins
Note2:
Please make
sure to cite these papers if you use Slipid/AMBER force field.
1-
Joakim P. M. Jämbeck
and Alexander P. Lyubertsev, "Derivation and Systematic Validation of a
Refined All-Atom Force Field for Phosphatidylcholine Lipids",J.
Phys. Chem. B, 2012, 116, 3164-3179.
2- Joakim P. M.
Jämbeck and Alexander P. Lyubertsev, "An Extension and Further
Validation of an All-Atomistic Force Field for Biological Membranes" J.
Chem. Theory Comput., 8, 2938-2948.
3- Joakim P. M.
Jämbeck and Alexander P. Lyubertsev, "Another Piece of the Membrane
Puzzle: Extending Slipids Further" J. Chem. Theory Comput., DOI:
10.1021/ct300777p.
|
Bioinformatics
Research Group
Faculty of Biological Sciences
Tarbiat Modares University
All
rights reserved. |
Contact S.
Shahriar Arab:
sh.arab@modares.ac.ir |