Proteins and bilayers

DAFT - Docking Assay For Transmembrane Components

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Last Updated: Wednesday, 22 April 2015 11:41

daft.tgz

DAFT is a method for investigating protein-protein and protein-lipid interactions by running many association simulations. These allow identifying the binding hotspots and alternative binding sites.

DAFT is a bundle of programs and supporting files, and comprises martinize, martinate, insane, and several MARTINI interaction table generating Python scripts, toghether with the standard lipid, ion and solvent topologies. The user interface is formed by the bash script daft.sh (see daft.sh -h for more information).

More background on this DAFT approach can be read in the DAFT paper: DOI: 10.1021/ct5010092

 

Flux calculator

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Last Updated: Wednesday, 07 February 2018 16:33

fluxer.py

This tool calculates fluxes across either a whole bilayer or through a defined channel. The trajectory must have been treated with -pbc nojump and, if analyzing the flux through a channel, care must be taken to ensure the channel is kept whole in the trajectory (use -pbc cluster).

Please cite J. Am. Chem. Soc., 2017, 139 (7), pp 2664–2671 whenever using results generated by fluxer.py.

Check the script's project page for more information on usage and to submit bugs.

seq2itp

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Last Updated: Thursday, 22 August 2013 10:01

A perl script to build your own peptide/protein topology (.itp). Use the -h option to see what it can do. As input it requires the amino acid sequence (.seq) and the secondary structure information (.ssd). Check out also the toy peptide example on the application page.

seq2itp.pl (version 1.1.5)
martini_v2.1_example.seq
martini_v2.1_example.ssd

 

atom2cg

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Last Updated: Thursday, 22 August 2013 10:01

A simple awk script that converts an atomistic PDB file to a coarse grained PDB file.

atom2cg_v2.1.awk

 

molmaker.py: Create molecule coordinates from their .itps

Details
Last Updated: Monday, 15 February 2016 17:57

molmaker.py

This tool creates a .gro from an .itp file. It works by randomly scattering coordinates along a linear stretch and then performing an evil minimization as VdW and charges are faded in (using the free energy code). As you already guess, it's totally useless for proteins unless you want a linear segment (in which case it works pretty well!).

Additionally, molmaker.py will likely not preserve your chiral centers unless you protect them in your topology using some sort of dihedral potential/restraint. Alternatively you might want to hand-correct each center using other tools and then energy-minimizing.

Check the -h flag for more details. Please report bugs in the GitHub project.