Takes an N-glycosylated glycoprotein in Gromacs generated with the Glycam forcefield and systematically generates a feasible configuration of N-glycans. This is accomplished via rigid rotation about three bonds per N-glycan.
- Python3
- Gromacs 5.1
Download and add the bin directory to $PATH. For example, in Linux, add
export PATH="/path/to/GlyRot/bin":$PATH
in ~/.bashrc and open a new terminal.
A precompiled binary using Gromacs 5.1 is provided in the bin directory. GlyRot must be executed while Gromacs 5.1 is installed. More than likely, the GlyRotHelper executable must be rebuilt. A Makefile is provided in the top directory, which can be built using make. GlyRotHelper uses source files only included in the original Gromacs 5.1 installation. For this reason, the Makefile must be edited to contain the src directory of the original Gromacs 5.1 package. For example, if the original Gromacs 5.1 package was downloaded and extracted to /home/username/gromacs/gromacs-5.1, then the include line should look like INCLUDE=/home/username/gromacs/gromacs-5.1/src. Additionally, the Makefile is provided assuming gromacs is not built with mpi. If building with mpi, libgromacs needs to be changed to libgromacs_mpi.
Execute GlyRot.py -h for a brief description of arguments. Defaults values are provided for optional arguments.
Starting in the top directory:
cd example
GlyRot.py -gro BChEG_GMX.gro -top BChEG_GMX.top -dtheta 90.
This assumes the gromacs executable is gmx. Otherwise, the -gex option should be used to specify a different gromacs executable name. If GlyRot was successful, the file Rotated.gro is generated. One can verify the glycans are sterically clashed in BChEG_GMX.gro, and not in Rotated.gro. The rotation resolution -dtheta 90 is used here to permit rapid execution on a personal computer. For actual system preparation, the default -dtheta 15 is advised, which generates glycan configurations at a rate of approximately 1 glycan per 15 minutes on a single CPU. Additional CPUs will not significantly improve this speed. BChEG_GMX.gro contains the coordinates of fully glycosylated human butyrylcholinesterase (9 glycans), and was used in this study.
An example script for executing GlyRot.py using Slurm on an HPC cluster is provided in srun_rot.sh. The script is executed using sbatch srun_rot.sh.
GlyRot is executed on Gromacs coordinate and topology files using the Glycam forcefield. These input files may be generated using Acpype on a system built using Glycam Web and AmberTools Leap. GlyRot was designed for use on glycoproteins downloaded without minimization from Glycam Web.
The three bonds that the N-glycans are rotated about are ND2 - C1, CB - CG, CA - CB. Atom names provided using the Glycam forcefield. All atoms correspond to the connected asparagine, except C1, which corresponds to the first attached sugar of the corresponding glycan. Each glycan is sequentially rotated using all rotamers about the three bonds, totaling (360/dtheta)3 rotamers per glycan. The minimum in-vacuo energy rotamer for each glycan is selected at each stage. This method has been shown to generate feasable glycan conformers even for densely glycosylated proteins, such as butyrylcholinesterase.