Peptides

Collagen Triple Helix

Collagen triple helix in vacuum

(provided by Markus Buehler)

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

Actin with ADP and ATP

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!

Toy peptide

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.

toypeptide.gro
toypeptide.mdp
toypeptide.top
toypeptide.itp

Amyloid Fibrils

(provided by Jesper Sorensen)

Equilibrated at T=300K, constant pressure P=1 bar.
System size: 27 hiAPP (human islet amyloid polypeptide) fibrils,  59271 waters

fibril.gro
fibril.mdp
fibril.top
fibril.itp