Specific topologies

Topologies for the cofactors associated with the Photosystem II. The ZIP-archives contain CG Martini topologies as well as united atom Gromos topologies for: Plastoquinone, Plastoquinol, Ubiquinone, Ubiquinol, Beta-carotene*, Heme b, Chlorophyll A and Pheophytin. Details on the parameterization and behavior of the topologies can be found in:

Atomistic and Coarse Grain Topologies for the Cofactors Associated with the PhotoSystem II Core Complex; Djurre H. de Jong, Nicoletta Liguori, Tom van den Berg, Clement Arnarez, Xavier Periole, and Siewert J. Marrink, J. Phys. Chem. B, 2015, 119 (25), pp 7791–7803 (10.1021/acs.jpcb.5b00809).


topologies.zip
 
 
 

*The file describing the tabulated angle of Betacarotene does not have the right format. Although it does  produce the right distribution, the dynamics are off. The tabulated potential and the ITP file below do have the right format, produce the right distribution and give better dynamics as compared to the atomistic simulations. Thanks to Floris van Eerden for pointing this out and providing us with the correct files.

BCR_correct.zip

 
 

Various saturated and unsaturated alkanes, alcohols, triglycerides, and many small organic solvents.

martini_v2.0_solvents.itp (updated: 07-06-2017)

 

Martini 2.2 N-Glycans

Topologies for Martini 2.2 glycans are available for download here, courtesy of César López Bautista and co-workers. See the publication for more information.

 

 

Common mono- and disaccharides, and amylose.

martini_v2.0_sugars.itp

 

 

Beta-cyclodextrin, Dimethyl-cyclodextrin and Hydroxypropyl-cyclodextrin

The user needs to incorporate a new bead type in the case of beta cyclodextrin which is included in the martini_v2.1_pc.itp included in the package. Beta cyclodextrin is represented as a dimer, since it is the most populated type in solution. However it can be easily transformed into a monomer if necessary.

When using this model please cite:

López, C. A., de Vries, A. H., & Marrink, S. J. Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes. Scientific Reports, 3, 2071 (2013). http://doi.org/10.1038/srep02071

cyclodextrin.tgz

Molecules not fitting in other categories.

Currently contains topologies for voltage-sensitive dyes

martini_v2.0_other.itp

Contains five commonly used phytochemicals

martini_v2.0_phytochemicals.itp
 

Optimal Martini 2 Cholesterol with LINCS

Optimized cholesterol model for Martini 2 to overcome the constraint convergence issues using LINCS.

 Details can be found in the publication:
B. Fábián, S. Thallmair, and Gerhard Hummer: Optimal bond constraint topology for molecular dynamics simulations of cholesterol. J. Chem. Theory Comput., 2023. DOI: 10.1021/acs.jctc.2c01032)
 
 
 
 

Artificial light harvesting dye (C8S3) for Martini 3

The parameters are for an artificial light harvesting dye (C8S3) which self-assembles into hollow nanotubes. Included are a gro and an itp for C8S3, a unit cell of the brickwork and herringbone formation, the script to make the cylinders, one nanotube and a bundle.

 
Details can be found in the publication:
Patmanidis et al., Nanoscale Advances, 2022, in press.
 

 

Nucleotide Cofactors for Martini 2

Thanks to the great work of Filipe Sousa and the Melo team, we can present to you nucleotide cofactors for Martini 2. This work includes topologies for key metabolites and cofactors, such as FAD, FMN, riboflavin, NAD, NADP, ATP, ADP, AMP, and thiamine pyrophosphate, in different oxidation and protonation states as well as smaller molecules derived from them (among others, nicotinamide, adenosine, adenine, ribose, thiamine, and lumiflavin), summing up a total of 79 different molecules.

Download here!

PSII cofactors

Topologies for the cofactors associated with the Photosystem II. The ZIP-archives contain CG Martini topologies as well as united atom Gromos topologies for: Plastoquinone, Plastoquinol, Ubiquinone, Ubiquinol, *Beta-carotene, Heme b, Chlorophyll A and Pheophytin. Details on the parameterization and behavior of the topologies can be found in:

Atomistic and Coarse Grain Topologies for the Cofactors Associated with the PhotoSystem II Core Complex; Djurre H. de Jong, Nicoletta Liguori, Tom van den Berg, Clement Arnarez, Xavier Periole, and Siewert J. Marrink, J. Phys. Chem. B, 2015, 119 (25), pp 7791–7803.

topologies.zip

*The file describing the tabulated angle of Betacarotene does not have the right format. Although it does  produce the right distribution, the dynamics are off. The tabulated potential and the ITP file below do have the right format, produce the right distribution and give better dynamics as compared to the atomistic simulations. Thanks to Floris van Eerden for pointing this out and providing us with the correct files.

BCR_correct.zip

 

DIM (Phthiocerol dimycocerosate) lipids

(provided by Matthieu Chavent - This email address is being protected from spambots. You need JavaScript enabled to view it.)

The coordinates and topological files for the DIM lipids for AMBER and MARTINI as well as  tcl (VMD) scripts and jupyter notebooks used to perform analysis can be accessed via the link:

https://github.com/MChavent/DIM_data/tree/master/MD_simulations

  The associated paper is available on Biorxiv preprint:   

https://www.biorxiv.org/content/10.1101/649541v1

Details
Last Updated: Thursday, 12 June 2014 15:13

Including all common PC and PEs, with hexanoyl, lauroyl, palmitoyl, oleoyl, stearoyl, linoleyl, and arachidonoyl tails. Trial topologies for a sphingolipid, ceramide, and for PG and PS lipids are also included. Lipids with two heads (bolalipids) are available as well.

martini_v2.0_lipids.itp

And here you can find the glycolipids, including MGDG, DGDG, PI, PIPs, GM1 and more ....

martini_v2.0_glycolipids.itp  (10 Oct 2013 - fix of PIP1 and GCER parameters)

martini_v.2.0_glycolipids_old2.itp (13 Sep 2013 - fix of GM1 and PIP2 parameters)

martini_v2.0_glycolipids_old.itp