This tool is moved to gmx_clusterByFeatures as sub-command hole.

gmx_clusterByFeatures is easy to install by one command: sudo pip3 install gmx-clusterByFeatures. hole command is same as gmx_hole. HELP and USAGE for gmx_clusterByFeatures hole is provided in this link. Moreover, gmx_clusterByFeatures include holeplot, which can be used to plot the data obtained from hole.

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gmx_hole

It can be used to calculate radius of protein channel/cavity for GROMACS MD trajectory. gmx_hole uses HOLE program to calculate radius of cavity/channel and dumps the output to a text file as a function of tiime. It also extract channel's outlining residues and dumps to same output file. This output file can be further read to perform final statistcal operations and plotting.

Please cite the original publication of hole:

O.S. Smart, J.M. Goodfellow and B.A. Wallace (1993). The Pore Dimensions of Gramicidin A. Biophysical Journal 65:2455-2460.

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Requirements

• To compile and install, GROMACS libraries are required. Presently, Gromacs 4.5.x, 4.6.x, 5.0.x, 5.1.x, 2016.x and 2018.x versions are supported.
• To use gmx_hole, HOLE program should be already installed.

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Download

git clone /~https://github.com/rjdkmr/gmx_hole

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Installation

cd gmx_hole
mkdir build
cd build
export CMAKE_PREFIX_PATH=/path/to/installed/gromacs/directory
cmake .. -DCMAKE_INSTALL_PREFIX=/opt/gmx_hole
make
make install

If fftw library libfftw3f.so or libfftw3f.a are not present in standard locations:

-DFFTW_LIB=/path/to/fftw3/lib

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Usage

To calculate channel radius using hole program. HOLE program should be already installed and present in $PATH environment variable.

gmx_hole -h

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