Analysis
ProLint
Prolint2 is an optimized tool for analyzing and visualizing lipid-protein interactions from molecular dynamics trajectories at coarse-grained or atomistic resolution.
For more details and to download the latest version, visit the [GitHub repository].
MDVoxelSegmentation
When working with large systems containing multiple bilayers or other dynamic macroscopic objects, it tends to come more natural to give these aggregates an identity of their own. This is exactly what MDAVoxelSegmentation does for amphipathic Martini systems. It not only detects bilayers/leaflets or other aggregates using a voxel based architecture, but it also keeps track of such entities over time.
For more details and to download the latest version, visit the [GitHub repository].
Rendering CG bonds & constraints with VMD
cg_bonds-v5.tcl is a Tcl script to read and draw Martini bonds and constraints in VMD. The bonds of the elastic networks can be drawn as well. The script for use with gromacs 5 can be found [here].
Usage
The script is invoked from the VMD command line. After sourcing it (source /path/to/cg_bonds.tcl, or /path/to/cg_bonds-v5.tcl), simply type cg_bonds (options and default values listed below). You can summon an “how to” at any moment by calling the cg_bonds_usage command.
This script uses the gmxdump executable compiled with gromacs. By default, it looks for it in the /usr/bin directory; you can specify another path with a specific option (see below). The script can now parse .top and .itp files, via the -top option.
cg_bonds
Options and default values (slightly different from the previous version!):
| -molid | “top” |
VMD-defined ID of the molecule to process |
| -gmx | /usr/bin/gmxdump |
absolute path to gmxdump executable (for version 5, this should point to the gmx executable, default /usr/bin/gmx) |
| -tpr | topol.tpr |
absolute path to the simulation file (.tpr) |
| -top | topol.top |
absolute path to the system topology files (.top linking to .itp) |
| -topoltype | “martini” |
protein topology type: “martini”, “elastic” or “elnedyn” |
| -net | “martini” |
network to draw: “martini”, “elastic” or “both” |
| -bndrcnstr | “both” |
draw bonds AND/OR constraints “bonds”, “constraints” or “both” |
| -cutoff | 7.0 | cutoff for bonds (angstroms) |
| -color | “red” |
color (color name or VMD-defined ID) of elastic bonds |
| -mat | “Opaque” |
material for elnedyn bonds |
| -rad | 0.2 | radius of elastic bonds |
| -res | 6 | resolution of elastic bonds |
In most of the cases, if a “classical” cut-off is used for the elastic network (0.9nm), more than 12 bonds per atom are defined and VMD refuses to draw them. BUT this script replaces bonds by cylinders, and is able to draw the entire elastic network. Note that you have to modify the default cutoff value to see all the links defined by the elastic network.
Then you can remove Martini bonds with the cg_delete_martini_bonds; and the cylinders with the cg_delete_elastic_bonds. The only option for the previous three commands is the VMD-defined ID of the molecule to process (via -molid, default is “top”).
Known issues
- Bonds drawn for the elastic network don’t follow the dynamic of the protein; the 12-bonds-limitation of VMD obliges to draw them using cylinders, not regular bonds. Please drop a mail if you have a solution to fix that…
- Version of VMD should be superior to
1.8.5(excluded) to run this script properly. Tclneeds an empty line at the end of the files it reads (.topand.itp)!- On the same level,
Tclseems to understand differently the simple and double quotes… Please check that before shouting.
Example
user@machine $ vmd protein.gro
vmd > source /home/user/scripts/cg_bonds.tcl
vmd > cg_bonds -top system.top -topoltype "elastic"
vmd > cg_bonds -gmx /home/user/bin/gmx-4.5.4/bin/gmxdump -tpr dyn.tpr -net "elastic" -cutoff 12.0 -color "orange" -mat "AOChalky" -res 12 -rad 0.1 -topoltype "elastic"
vmd > cg_delete_elastic_bondsThe few lines above will:
- load the protein.gro structure,
- source the cg_bonds.tcl script,
- draw the martini bonds (using the .top file specified in the command line) extracted from a .top containingelastic network bonds,
- draw the elastic network with the options (cutoff, color, material, resolution and radius) specified by extracting the bonds from the .tpr file,
- delete the elastic network bonds previously drawn.
All these line will be applied to the molecule with the VMD-defined ID 0 (or “top”).