trj_cavity Icon

trj_cavity

5.0 Stars (2)
5 Downloads (This Week)
Last Update:
Download trj_cavity_v2.1.tar.gz
Browse All Files
Linux

Screenshots

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.

trj_cavity Web Site

Categories

Chemistry

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.

KEEP ME UPDATED

Other Useful Business Software

The Sight of Sound Icon

­ Improve VoIP Visibility from SIP to RTP

The Sight of Sound Icon
Cloudbased voice solutions are common in enterprise networks and frustrating for operations teams to manage. Simplify VoIP monitoring by having a proactive analysis of on-prem, hybrid and UCaaS voice services. Try the ThousandEyes VoIP monitoring solution today, free.

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
Write a Review

User Reviews

  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    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!

    Posted 04/02/2014
  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    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.

    Posted 03/31/2014
Read more reviews

Additional Project Details

Programming Language

C++

Registered

2013-12-18

Thanks for helping keep SourceForge clean.

Screenshot instructions:
Windows
Mac
Red Hat Linux   Ubuntu

Click URL instructions:
Right-click on ad, choose "Copy Link", then paste here →
(This may not be possible with some types of ads)

More information about our ad policies
X

Briefly describe the problem (required):

Upload screenshot of ad (required):
Select a file, or drag & drop file here.

Please provide the ad click URL, if possible:

Get latest updates about Open Source Projects, Conferences and News.

No, thanks