Download

The source code for Vina-Carb can be downloaded from here.

Contents of the Download

• Modified AutoDock Vina 1.1.2 which now include the CHI energy functions [2] and called Vina-Carb 1.0.
• Additional files: canonicals.txt, GLYLIB

Requirements for Installation

• A Linux- or UNIX-based operating system
• A GCC compiler
• Boost C++ libraries version 1.41.0: The Vina-Carb source code was compiled using this version of Boost libraries (as was the original AutoDock Vina 1.1.2). Using other versions of the libraries may work, but it has not been tested.
• The GNU make utilities
• Additionally:
  • The input carbohydrate file must follows standard carbohydrate nomenclature for atomnames.
  • The environment variable VINA_CARB should be set to point to the location of parent directory VC_1_0. Please provide the full path.

Installation

To compile Vina-Carb, follow the instructions for how to compile AutoDock Vina from source here. The executable file created will be called vina-carb.

Configuration file

Besides the flags regularly used during AutoDock Vina docking, the user can use two additional parameters to tweak the application of CHI energies during Vina-Carb docking as shown below; default values set are shown in square brackets.
chi_coeff [1.0]: this value can be adjusted to any number; a value of 0 will switch Vina-Carb to AutoDock Vina.
chi_cutoff [2.0]: this value can be changed to any number but with a value high enough (12), it would switch to AutoDock Vina as all CHI energy penalties will be negated.

Running the program

vina-carb –config config –log log.txt –out output_models.pdbqt

Associated Publications

1. Vina-Carb: Improving Glycosidic Angles During Carbohydrate Docking. Nivedha, Anita; Thieker, David; Makeneni, Spandana; Hu, Huimin; Woods, Robert. J. Chem. Theory Comput. 2016, 12 (2), pp 892–901. DOI: 10.1021/acs.jctc.5b00834
2. Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff. Nivedha, Anita; Makeneni, Spandana; Foley, B. Lachele; Tessier, Matthew B.; Woods, Robert J. J. Comput. Chem. 2014, 35, 526–539. DOI: 10.1002/jcc.23517