Quickstart RINRUS tutorial

This tutorial is a simplified version of the instructions pages to get you started with RINRUS. It shows how to run the RINRUS model building procedure in two ways: with the driver (recommended) or with the scripts individually.

The pre-processed PDB:2CHT structure 2cht_h_corrected_new.clean.pdb is provided in the examples directory of the GitHub repo.

cp ~/git/RINRUS/examples/2025-NEW-EXAMPLES/2cht_h_corrected_new.clean.pdb .

Using the driver

Create a text file called rinrus.inp containing one of the following sets of input options:

To build models from the probe RIN:

  pdb: 2cht_h_corrected_new.clean.pdb
  seed: A:203
  rin_program: probe
  model: max
  model_prot_ignore_ids: A:203
  qm_input_format: orca
  seed_charge: -2

To build models from the arpeggio RIN:

  pdb: 2cht_h_corrected_new.clean.pdb
  seed: A:203
  rin_program: arpeggio
  arpeggio_rank: counts
  model: max
  model_prot_ignore_ids: A:203
  qm_input_format: orca
  seed_charge: -2

To build models based on distance (e.g. atoms within 5A of the closest seed atom):

  pdb: 2cht_h_corrected_new.clean.pdb
  seed: A:203
  rin_program: distance
  dist_type: closest
  dist_max: 5
  model: max
  model_prot_ignore_ids: A:203
  qm_input_format: orca
  seed_charge: -2

Then run the driver with your input file:

python3 ~/git/RINRUS/bin/RINRUS_driver.py -i rinrus.inp

Running the scripts individually

Step 1: Selecting the active site/generating the active site RIN

The active site RIN can be determined from the seed fragments based on probe contacts, arpeggio contacts or distance. Pick one of these options:

Probe:

Run probe on the (modified) PDB file to generate a *.probe file of all contacts in the enzyme. Then extract the active site RIN from the probe contacts with probe2rins.py.

  ~/git/RINRUS/bin/probe -unformated -MC -self "all" 2cht_h_corrected_new.clean.pdb > 2cht_h_corrected_new.clean.probe

  python3 ~/git/RINRUS/bin/probe2rins.py -f 2cht_h_corrected_new.clean.probe -s A:203

Arpeggio:

Run arpeggio on the (modified) PDB file to generate a *.contacts file of all contacts in the enzyme. Then extract the active site RIN from the arpeggio contacts with arpeggio2rins.py.
```
  python3 ~/git/RINRUS/bin/arpeggio/arpeggio.py 2cht_h_corrected_new.clean.pdb

  python3 ~/git/RINRUS/bin/arpeggio2rins.py -f 2cht_h_corrected_new.clean.contacts -s A:203
```
Distance:
Use dist_rank.py to select all fragments with any atoms within a cutoff radius of the seed (here doing atoms within 5A of the closest seed atom)
```
  python3 ~/git/RINRUS/bin/dist_rank.py -pdb 2cht_h_corrected_new.clean.pdb -s A:203 -max 5 -type closest
```

Step 2: Structure trimming and capping

Run rinrus_trim2_pdb.py to trim the protein structure based on the atoms/functional groups selected in res_atoms.dat. Here we are making the “maximal” model with all selected groups included.

python3 ~/git/RINRUS/bin/rinrus_trim2_pdb.py -pdb 2cht_h_corrected_new.clean.pdb -s A:203 -model max

Then use pymol_protonate.py to cap the truncation sites with hydrogens. You must have a local copy of PyMOL installed! If you used arpeggio or distance ranking, you might have to change the model PDB filename in this command to match the size of those models.

python3 ~/git/RINRUS/bin/pymol_protonate.py -pdb res_14.pdb -ignore_ids A:203

Make the template model PDB file with make_template_pdb.py. The template PDB file is the capped model with the atom constraints encoded into it. Again here the model number might need to be changed for arpeggio/distance-based models.

python3 ~/git/RINRUS/bin/make_template_pdb.py -model 14

Step 3: Preparing input files for QM computations

Use write_input.py to generate input files for quantum chemistry packages. Again, make sure that the correct model PDB filename is used.

Create a gaussian input file:

  python3 ~/git/RINRUS/bin/write_input.py -pdb model_14_template.pdb -c -2 -format gaussian -inpn gau.inp

Create an ORCA input file:

  python3 ~/git/RINRUS/bin/write_input.py -pdb model_14_template.pdb -c -2 -format orca -inpn orca.inp

Create a Psi4 F-SAPT input file:

  python3 ~/git/RINRUS/bin/write_input.py -pdb model_14_template.pdb -c -2 -format psi4-fsapt -seed A:203 -inpn psi4-input.dat