This is the Linux app named trj_cavity to run in Linux online 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.
Download and run online this app named trj_cavity to run in Linux online with OnWorks for free.
Follow these instructions in order to run this app:
- 1. Downloaded this application in your PC.
- 2. Enter in our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.
- 3. Upload this application in such filemanager.
- 4. Start the OnWorks Linux online or Windows online emulator or MACOS online emulator from this website.
- 5. From the OnWorks Linux OS you have just started, goto our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.
- 6. Download the application, install it and run it.
SCREENSHOTS
Ad
trj_cavity to run in Linux online
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++
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.
