virion-spike-model

Generate HIV and SIV virion models with a given number of spikes and measure distances between spikes.

Author: Wonmuk Hwang ( hwm@tamu.edu ). see LICENSE.

Primary reference: Kemin Tan, Junjian Chen, Yu Kaku, Yi Wang, Luke Donius, Rafiq Ahmad Khan, Xiaolong Li, Hannah Richter, Michael S. Seaman, Thomas Walz, Wonmuk Hwang, Ellis L. Reinherz & Mikyung Kim Inadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility Nature Communications 14:7218 (2023). https://www.nature.com/articles/s41467-023-42097-6

---

Directories:

• [./inp1] Contains input files for execution of the code.
• [./example1]: Outputs of step 1 are written.
• [./data1]: Outputs of step 2) are written. Initially empty.
• [vmd]: VMD files for visualization.

---

How to run:

The following operations will render models in VMD and generate graphs used in Fig. 6 of the reference cited above.

0) Dependent package: Visual Molecular Dynamics (VMD).

VMD can be downloaded from: https://www.ks.uiuc.edu/Research/vmd/

1) To create a model virion to be visualized by VMD:

• In virion_main.cpp, uncomment line 13:

#define VMD // uncomment to write vmd file

• Compile:

g++ vector_stl.cpp ftn_virion.cpp virion_main.cpp -O3 -o a.out

• Run: The following will write outputs to ./example1

./a.out inp1/demo14g1.dat
./a.out inp1/demo14g3.dat
./a.out inp1/demo73g1.dat
./a.out inp1/demo73g3.dat

• Visualize using VMD:

cd vmd

vmd -size 1000 1000 -e view_demo_14g1-1.vmd
vmd -size 1000 1000 -e view_demo_14g3-1.vmd
vmd -size 1000 1000 -e view_demo_73g1-0.vmd
vmd -size 1000 1000 -e view_demo_73g3-0.vmd

2) To measure inter-spike distance distribution:

• In virion_main.cpp, comment out line 13:

//#define VMD // uncomment to write vmd file

• Compile:

g++ vector_stl.cpp ftn_virion.cpp virion_main.cpp -O3 -o a.out

• Run: The following will write outputs to ./data1

./a.out inp1/meas14g1.dat &
./a.out inp1/meas14g3.dat &
./a.out inp1/meas73g1.dat &
./a.out inp1/meas73g3.dat

• Create histograms:

python plot_histo_rcut1r.py
output: histo_rcut1r.pdf, ./data1/histo*_rcut.dat

python plot_histo_nn1.py
output: histo_nn1.pdf, ./data1/histo{14,73}.dat