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.

Project Samples

trj_cavity

Project Activity

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