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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.
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User Reviews
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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!
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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.