Soft Matter & Molecular Biophysics Group    

SUGAR-PIE: Scripted Utility to Get Atomic Resolution by Positional Interpolation/Extrapolation


SUGAR-PIE is an application developed and maintained by Ángel Piñeiro, designed for the easy mapping of lipid bilayers from coarse-grain (CG) to atomistic (AT) resolution based on an interpolation/extrapolation approach of atomic positions. The current version works with lipid bilayers based on POPC and/or DPPC. At the moment only the MARTINI force field is available for coarse-grain level. For atomic resolution several parameterizations of the GROMOS force field, the Berger parameterization of lipids, and the CHARMM36 force field are available. The list of considered force fields and molecules is expected to increase. Note that it is possible to introduce a mixture of both lipids and even a protein embedded or interacting with the bilayer. If a protein is included in the system you should also upload an atomistic PDB file for it. The mapping back method from CG to AT resolution is quick and simple but the current version does not map molecules other than POPC and DPPC. Thus, if your system includes a protein, its atomistic coordinates will be aligned and substituted with its coarse grain replica.

For any comment, please, contact: Angel.Pineiro at usc.es

Disclaimer: SUGAR-PIE was designed for educational or academic purposes only. If you intend to use this program for commercial purposes you should contact the authors. We do not accept any responsability for the results provided by this application. The personal data voluntarily provided by the user is for information purposes only.


Example: MARTINI POPC molecule backmapped to CHARMM36 all-atom force field using SUGAR-PIE.


STEP 1 (optional): Please, enter your name, institution and email :

User Name: Institution: E-mail:

STEP 2: Select the coarse-grain coordinates file (PDB or GRO format) to be mapped back to atomistic resolution. You can use this coarse grain DPPC bilayer if you want to test the application.
PLEASE, DO NOT INTRODUCE BROKEN MOLECULES THROUGHOUT THE PBC!!
Coarse grain PDB/GRO file: (max. size = 1 MB/file)

STEP 3: If your system contains a protein, it will NOT be transformed to atomistic resolution. In this case, it is required to upload an atomistic pdb file that will be aligned to the corresponding CG structure and included in the output files. Please, include an atomistic pdb file for your protein or go to the next step
Protein atomistic PDB file: (max. size = 1 MB/file)

STEP 4: Select the atomistic force field:
Berger + OPLS: Berger et al. Biophys. J. 72(5) 1997 2002-2013 & Chakrabarti et al. Biophys. J. 98(5) 2010 784-92
Berger + GROMOS 53A6: Berger et al. Biophys. J. 72(5) 1997 2002-2013 & Peter Tieleman web site
GROMOS 53A6 Kukol: Andreas Kukol J. Chem. Theo. Comput. 5(3) 2009 615-626
GROMOS 53A6L: Poger et al. J. Comput. Chem. 31(6) 2009 1117-1125 & ATB server
GROMOS 43A1-S3: Chiu et al. J. Phys. Chem. B 114(9) 2009 2748-2763 & 43A1-S3 force field files
CHARMM36: Klauda et al. J. Phys. Chem. B 114(23) 2010 7830-7843 & CHARMM36 force field files for GROMACS


This normally takes less than 5 min, depending on the chosen force field and system size.
If the number of lipids in your system is much larger than 200, please, feel free to contact us

ACKNOWLEDGEMENTS: We thank the GROMACS developers for their exceptional work since SUGAR-PIE is partially based on this program package. The lipid parameters were kindly provided by S. Khalid and T. Piggot, University of Southampton. This work is supported by grant MAT2011-25501 (MICINN, Spain).

REFERENCES: Please, cite this work: DOI: 10.1039/C2SM25877C if you use SUGAR-PIE. The mapping back method employed by SUGAR-PIE is simple and quick. More elaborated methods are available for the same aim. See for instance: (i) Andrzej J. Rzepiela, Lars V. Schafer, Nicolae Goga, H. Jelger Risselada, Alex H. De Vries, Siewert J. Marrink. Reconstruction of atomistic details from coarse-grained structures. Journal of Computational Chemistry, 31(6) 1333-1343, 2010. DOI: 10.1002/jcc.21415; or (ii) Phillip J. Stansfeld and Mark S.P. Sansom. From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations. Journal of Chemical Theory and Computation, 7(4) 1157-1166, 2011. DOI: 10.1021/ct100569y.

FUNDING: The present project was supported by the grant MAT2011-25501 (MINECO-Spain).