This directory contains example commands, scripts, and data files for the AASC package.

Contained are the following:

  - 173_SM_PQRS/                        : Directory of all small molecule pqr files used in "A closed-form, analytical approximation for apparent surface charge and electric
field of molecules"
  - LARGER_STRUCTURES/                  : Directory with structure files and contact residues lists for the 6M0J complex.
  - calculate_sm_ef-asc.sh              : Script that computes small molecule electric field/apparent surface charge .gvert/gface files for all structures in 173_SM_PQRS/, which can be visualized with the graphical GEM package ( See https://people.cs.vt.edu/onufriev/software.php ). Files are stored in "sm_ef_files" and "sm_asc_files", respectively.
  - calculate_sm_hydration_energies.sh  : Script that computes small molecule hydration energies for all structures in 173_SM_PQRS/. The result is placed in "173_sm_hydration_energies".
  - calculate_6M0J_A-E_ASC.sh           : Script that computes Receptor and Spike receptor binding domain (RBD) apparent surface charge, using a list of contact residues within 3.8 \AA of each chain.
  - cleanup.sh                          : Script to clean up generated files through EXAMPLES/

Below are stand-alone command lines that describe simple applications of the AASC package:

../build/aasc 173_SM_PQRS/123_trimethylbenzene.pqr 80 1

- Computes the solvation energy of the molecule "123_trimethylbenzene", with an inner/outer dielectric constant of 1 and 80, respectively.

RESULT:
"
This file is 22 lines long.
This molecule contains 1 residues and 21 atoms.
Total molecular charge: 0.00
Running NanoShaper with given parameters
Found surfaces, continuing.
The estimated electrostatic radius (A) of this molecule is : 3.328537
Solvation Energy is : -3.287239
"

../build/aasc 173_SM_PQRS/123_trimethylbenzene.pqr 80 1 --total_surface_charge

- Passing "--total_surface_charge" computes total surface charge of the structure from triangular surface area and computed apparent surface charge. As the outer dielectic constant tends to infinity, the total surface charge will tend to the sum of atomic charges, providing a "sanity check" on our method.

RESULT:
"
This file is 22 lines long.
This molecule contains 1 residues and 21 atoms.
Total molecular charge: 0.00
Running NanoShaper with given parameters
Found surfaces, continuing.
The estimated electrostatic radius (A) of this molecule is : 3.328537
Total Surface Charge is : 0.004219
Solvation Energy is : -3.287239
"

../build/aasc LARGER_STRUCTURES/6M0JA.pqr 80 1 --nanoshaper_config_file=LARGER_STRUCTURES/6M0JA.conf --water_probe_radius=2 --triangulation_density=10 --projection_length=0.7 --residue_list=LARGER_STRUCTURES/6M0JA_contacts --write_asc

- Computes apparent surface charge 0.7 \AA away from the ACE2 receptor RBD of the 6M0J complex.
NanoShaper configuration is given in "LARGER_STRUCTURES/6M0JA.conf".
A larger water probe radius of 2 \AA is used, as compared to the default of 1.4 \AA.
Triangulation density is increased to a 0.1 \AA NanoShaper grid, as compared to the default 0.5 \AA grid.
The residue contact list is taken from "LARGER_STRUCTURES/6M0JA_contacts".

- Visualization can be undertaken with the graphical GEM package ( See https://people.cs.vt.edu/onufriev/software.php ). Utilizing the same parameters as the above command line, use the "readVertices" parameter in addition to "-visualize" to input AASC computed .gvert/.gface files. The full command line tested (after renaming 6M0JA_asc.g{vert.face} to 6M0JA.g{vert.face}, to be read by the graphical GEM) is:

 gemg 6M0JA 80 1 0 -visualize -readVertices -fixColors 0.008

NOTES:

- .gvert/.gface files are, by default, placed in the directory of the given .pqr file.
- When a configuration file is provided, triangulation configure options in AASC do not do anything - all these options are assumed to be given in the configuration file.
- .face/.vert file visualization is the standard MSMS format, supported by Visual Molecular Dynamics (VMD https://www.ks.uiuc.edu/Research/vmd/).
