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https://github.com/unixjunkie/mmo
Molecular Mechanics in OCaml
https://github.com/unixjunkie/mmo
ani-2x docking ligand molecular-mechanics monte-carlo ocaml-library ocaml-program protein universal-force-field
Last synced: 2 months ago
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Molecular Mechanics in OCaml
- Host: GitHub
- URL: https://github.com/unixjunkie/mmo
- Owner: UnixJunkie
- License: bsd-3-clause
- Created: 2024-02-22T04:45:15.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2024-04-19T01:36:53.000Z (8 months ago)
- Last Synced: 2024-04-19T02:37:18.260Z (8 months ago)
- Topics: ani-2x, docking, ligand, molecular-mechanics, monte-carlo, ocaml-library, ocaml-program, protein, universal-force-field
- Language: OCaml
- Homepage:
- Size: 1.46 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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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:
[](https://doi.org/10.5281/zenodo.10682034)
## To compile the software
Tested on Ubuntu Linux 24.04 w/ ocaml-4.14.1.
On Linux or a UNIX-like:
```bash
mkdir -p ~/src
cd src
git clone https://github.com/UnixJunkie/MMO.git
cd MMO
sudo apt install opam
opam init
eval `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.
```bash
~/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:
```bash
~/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:
```bash
./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
```