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README.md

vinaSH

VinaSH: Improved Autodock Vina that accounts for Sigma Hole interactions.

Citation: If you you use vinaSH. Please cite the following manuscript. "S---O, S---N sulfur bonding interactions in Protein-Ligand Complexes: Empirical Considerations and Scoring Function” Journal of chemical Information and modeling, 2016, 56 (12), pp 2298–2309

VinaSH Installation Instructions:

  1. Download VinaSH from https://github.com/ssirimulla/vinaSH or from http://www.sirimullaresearchgroup.com/software.html
  2. Save the VinaSH directory in file system at a location of your choosing. Windows Compatibility VinaSH is expected to work on Windows XP and newer systems. Installing Download the vinaSH.exe from the Windows folder into the desired location Running Open the Command Prompt and go to the folder where you downloaded the executable and run vinaSH.exe --help Linux Compatibility VinaSH is expected to work on x86 and compatible 64-bit Linux systems. Installing Download the executable file in the linux folder to the desired location Running In a terminal window, go to where you downloaded the executable and run ./vinaSH --help If you get a permissions denied message, use the command: chmod +x vinaSH Alternatively, before downloading the executable, you can go to the directory you wish to work and use the command git clone https://github.com/ssirimulla/vinaSH.git Then navigate to the linux folder and run ./vinaSH --help Mac Compatibility VinaSH is expected to work on Mac OS X 10.6 (Snow Leopard) through 10.10 (Yosemite) Intel machines. Installing Download the executable file in the mac folder to the desired location Running In a terminal window, go to where you downloaded the executable and run ./vinaSH --help If you get a permissions denied message, use the command: chmod +x vinaSH Alternatively, before downloading the executable, you can go to the directory you wish to work and use the command git clone https://github.com/ssirimulla/vinaSH.git Then navigate to the mac folder and run ./vinaSH --help Building from source Step 1: Install a C++ compiler suite On Windows, you may want to install Visual Studio; on OS X, Xcode; and on Linux, the GCC compiler suite.

Step 2: Install Boost Install Boost. (Version 1.57.0 was used to compile the official binaries. With other versions, your luck may vary)

Step 3: Build Vina If you are using Visual Studio, you may want to look at this tutorial for compiling: https://sites.google.com/site/mkoohim/stories/how-can-compile-autodock-vina-in-visual-studio. For optimal performance, remember to compile using the Release mode. On OS X and Linux, you may want to navigate to the appropriate build subdirectory, customize the Makefile by setting the paths and the Boost version, and then type: make depend And then type: make 3) VinaSH needs supporting visualization programs for preparation and viewing of molecules. These can be downloaded from any compatible 3rd party: a. Some examples are given below MGL Tools (http://mgltools.scripps.edu/downloads) Pymol (https://www.pymol.org/) 4) Once VinaSH and associated programs are downloaded you are ready to start preparing files to run 5) This program is very similar to the base program AutoDock Vina, for any further information needed please refer to the Scripps Research Institute manual for AutoDock Vina. http://vina.scripps.edu/manual.html

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