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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- To compile and install, GROMACS libraries are required. Presently, Gromacs 4.5.x, 4.6.x, 5.0.x, 5.1.x and 2016.x versions are supported.
- To use
gmx_hole
, HOLE program should be already installed.
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git clone https://github.com/rjdkmr/gmx_hole
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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
orlibfftw3f.a
are not present in standard locations: -DFFTW_LIB=/path/to/fftw3/lib
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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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