README

MMO: Molecular Mechanics in OCaml

Some code for flexible ligand / rigid protein calculations.

Warning: this code is prototypical in nature. Maybe, part of it will be released as a proper standalone library in the long-term (the Mol and Mol2 modules plus their dependencies).

Dataset

The dataset that was produced using this software can be downloaded from:

To compile the software

Tested on Ubuntu Linux 24.04 w/ ocaml-4.14.1.

On Linux or a UNIX-like:

mkdir -p ~/srccd srcgit clone https://github.com/UnixJunkie/MMO.gitcd MMOsudo apt install opamopam initeval `opam env --shell=bash`opam pin add mmo .make

How to score a ligand conformer w/ psi4 (true QM calculation)

This requires mayachemtools and psi4 to be installed.

~/src/MMO/bin/psi4_ene.sh ligand.sdf

How to score a ligand conformer w/ ANI-2 (approximated QM)

This requires the Python package torchani to be installed:

~/src/MMO/bin/QM_score_mol2.sh ligand.mol2

How to run a MC simulation in dihedral space to minimize a docked ligand using ANI-2?

If you have compiled the software and you have torchani installed, you can run:

./lds -f --no-interp --ligand-only --intra-QM -lig docked_ligand.mol2 \  -rec prot_rec.pqrs -roi prot_ROI.bild -steps 10k --ene 50 --no-compress --out-dir MC10kQM

1. cpm
2. nlopt
3. cppo
4. ocamlgraph
5. pyml
6. bitv
7. genspir
8. base-bigarray
9. vector3
10. parany>= "14.0.0"
11. ocaml>= "4.14.1"
12. minicli>= "5.0.0"
13. line_oriented
14. dune>= "1.11"
15. dolog>= "5.0.0"
16. bst>= "2.0.0"
17. batteries>= "3.5.0"

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