trj cavity

We have hosted the application trj cavity in order to run this application in our online workstations with Wine or directly.

Quick description about trj cavity:

trj_cavity finds protein cavities throughout Molecular Dynamics (MD) simulation trajectories. The program works with files in PDB format, but it also can read/generate GROMACS compatible formats such as XTC.

The same project can be compiled as a GROMACS tool or as a standalone version. Installation instructions are provided in the INSTALL file of the project and in https: //sourceforge.net/p/trjcavity/wiki/Home/#ffad

If you need support using this tool (or report bugs), please post it in the discussion forum.

Remarks: v2 runs in parallel and supports GROMACS v5.1+ series. If you want to continue on using GROMACS v4.x, please use trj_cavity_v1.1.

Features:

• Finds protein cavities in MD simulation trajectories.
• Produces MD trajectories of protein cavities vs time.
• Provides statistics of protein cavity distribution.
• Calculates cavity volume descriptor.
• Normal axis pore tunnel radius profile.

Programming Language: C++.
Categories: