Peptides

Bacterial cell wall peptidoglycan

Details: Last Updated: Wednesday, 28 October 2020 14:57

A Martini model of bacterial cell wall peptidoglycan is now available, thanks to the nice work of Vaiwala et al. Download the files here!

Any queries regarding the model should be addressed to the authors (see below).

The zip-archive contains the forcefield parameters (.itp) files and the structure (.gro) files of the single, 7, and 21 chains conformer for the peptidoglycan layer of the bacterial cell envelope, along with the README file. The details for the parameterization can be found in:

Rakesh Vaiwala, Pradyumn Sharma, Mrinalini Puranik, K. Ganapathy Ayappa. Developing a Coarse-Grained Model for Bacterial Cell Walls: Evaluating Mechanical Properties and Free Energy Barriers, J. Chem. Theory Comput. 2020, 16, 8, 5369–5384

KALP in a DPPC bilayer

Details: Last Updated: Thursday, 22 August 2013 09:41

KALP (23 residue) in a DPPC bilayer

kalp_DPPC.mdp

kalp_DPPC.top

kalp.itp

kalp_DPPC.gro

Collagen Triple Helix

Details: Last Updated: Thursday, 07 May 2015 14:19

Collagen triple helix in vacuum

(provided by Markus Buehler)

Note: the required 'collagen.itp' file can be generated using the martinize script

collagen.mdp

collagen.top

collagen.gro

HA fusion peptides

Details: Last Updated: Thursday, 22 August 2013 09:41

Hemagglutinin (HA) fusion peptides at lipid interface

Topologies for the wildtype at pH 5.0 and pH 7.4, and mutants W14A and G1V,

and coordinate files for a system of 256 DOPE lipids with 4 WT peptides

either in a randomized solution or in a stalk-phase

WT_pH5.0.itp

WT_pH7.4.itp

W14A.itp

G1V.itp

mixed_4WTpH5.0.top

mixed_4WTpH5.0.gro

stalkphase_4WTpH5.0.top

stalkphase_4WTpH5.0.gro

Actin with ADP and ATP

Details: Last Updated: Wednesday, 26 February 2020 16:47

Interested in using Martini for ADP or ATP with actin?

The attached .zip -file contains topologies for ADP, ATP as well as ADP-actin and ATP-actin systems. PDB files are provided for ADP- and ATP-actin, as well as the F-actin strand. As an added bonus, there's a short bash script which allows the user to build fibers of arbitrary lengths from one of the PDB files (2zwh.pdb).

Download the files here!

Glycophorin in DPPC membrane

Details: Last Updated: Thursday, 22 August 2013 09:41

Glycophorin A monomer in a DPPC bilayer. These simulations have been ran with an older, unpublished version of the MARTINI forcefield. Use with the greatest care.

gly_A_monomer_DPPC.mdp

gly_A_monomer_DPPC.top

gly_A_monomer.itp

gly_A_monomer_DPPC.gro

MscL in a bilayer

Details: Last Updated: Thursday, 22 August 2013 09:41

MscL channel embedded in a DOPC bilayer

(both an open and closed state are provided)

mscl.mdp

mscl.top

mscl.itp

mscl.ndx

mscl-closed.gro

mscl-open.gro

Toy peptide

Details: Last Updated: Thursday, 22 August 2013 09:41

The toy peptide contains all amino acids.
Half of the peptide is helical, the other half beta strand.
Equilibrated at T=300K, P=1 bar.
System composition: 1 peptide, water 1538.