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

Project Activity

See All Activity >

Categories

Chemistry

Follow trj_cavity

trj_cavity Web Site

Other Useful Business Software

Communicate & Connect with Ring Central's VoIP Solution Communicate & Connect with Ring Central's VoIP Solution Icon
Communicate & Connect with Ring Central's VoIP Solution Icon

Cloud Powered Business Phone System

  • Unrivaled value & reliability in one solution
  • Unlimited Calls/SMS/Conferencing/Fax
  • Trusted by 350,000+ Businesses

Rate This Project

Login To Rate This Project

User Ratings

★★★★★
★★★★
★★★
★★
2
0
0
0
0
ease 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 5 / 5
features 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 5 / 5
design 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 5 / 5
support 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 5 / 5

User Reviews

  • bipinsingh, I have moved your review to the discussion forum since this page doesn't allow me to reply to reviews. Many thanks for your comments!

  • I have two commnets: (1) As mentioned in the abstract of the JCTC paper that stand-alone, GROMACS-independent version is also available at the same address, but could not locate the same. Can you please help me in this regard. (2) I tried the trj_cavity on my system after compiling the source code but it result in following error: "Segmentation fault (core dumped)" Please give your suggestions.

Read more reviews >

Additional Project Details

Programming Language

C++

Registered

2013-12-18