This is the Linux app named trj_cavity whose latest release can be downloaded as trj_cavity_v2.1.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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trj_cavity
DESCRIPTION
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
This is an application that can also be fetched from https://sourceforge.net/projects/trjcavity/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
