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This repository contains code and data to reproduce the figures in the paper "Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents"

Data in this repository

In the paper, we ran REST2 simulations of 11 compounds, 4 force fields, partially in several solvents, and partially with 2 different settings. The nomenclature is as follows:

  • 11 compounds: BC1 (begnini-compound-1, residue name BC1), BC2 (begnini-compound-2, BC2), G16 (poongavanam-g16, G16), E2-enant (poongavanam-e2-enant, PE2), rifampicin (danelius-rifampicin, RIF), roxithromycin (danelius-roxithromycin, ROX), telithromycin (danelius-telithromycin, TEL), spiramycin (danelius-spiramycin, SPI), lorlatinib (peng-lorlatinib, LOR), NLeu5R (comeau-nleu5r, N5R), NLeu5S (comeau-nleu5s, N5S). Some compounds are protonated in water: rifampicin (danelius-rifampicin-charged), roxithromycin (danelius-roxithromycin-charged), telithromycin (danelius-telithromycin-charged), spiramycin (danelius-spiramycin-charged)
  • forcefield: OpenFF 2.0 (openff), GaFF 2 (amber), OPLS/AA (opls), XFF with DASH charges (xff-dash)
  • method: REST2 with quadratic lambda placement (hremd-quadratic), REST2 with exponential lambda placement (hremd-exponential)
  • solvent: chloroform (chcl3), water (water), DMSO (dmso)

Reproducing the Figures

All figures can be reproduced by following these steps:

  • clone this repository: git clone [email protected]:rinikerlab/macrocycle-ff-validation.git
  • create a new environment:
conda env create -f environment.yml
conda activate macrocycle-ff-benchmark
  • Run the notebook code/Create-Figures.ipynb

Re-running simulations

The data folder contains solvated topologies and .gro files for each combination of compound, solvent, and force-field. To re-run a simulation, follow the following steps:

  • create a folder data/COMPOUND/SOLVENT/equilibrate/FORCEFIELD, and copy the content of code/md_templates/equilibrate there.
  • set all placeholders in equilibration.sh, and run it. FORCEFIELD and SOLVENT_LC should be replaced to a name matching the folder structure ("openff" / "amber" / "opls" / "xff-dash" and "water" / "chcl3" / "dmso"), and SOLUTE should match the residue name in the topology.
  • create a folder data/COMPOUND/SOLVENT/hremd-quadratic/FORCEFIELD, and copy the content of code/md_templates/hremd-quadratic there.
  • set all placeholders in 1-get-inputs.sh, and execute the scripts in the order 1-4. Use 4-run-local.sh to run on the current PC. 4-run-euler.sh is the submit script that was used on the ETH Euler cluster, and might be used as a template to run on other cluster systems.

As an example, you can run the following to start one equilibration + REST2 simulation (after cloning this repository, starting from the base folder)

CMP=poongavanam-e2-enant
CMP_NAME=PE2
FF=amber
SOLV=dmso

# Equilibration
eq_dir=data/$CMP/$SOLV/equilibrate/$FF
mkdir -p $eq_dir
cp code/md_templates/equilibrate/equilibrate.sh $eq_dir/ || exit 1
( cd $eq_dir
	sed -i "s/FORCEFIELD=.*/FORCEFIELD=$FF/;s/SOLVENT_LC=.*/SOLVENT_LC=$SOLV/;s/SOLUTE=.*/SOLUTE=$CMP_NAME/;" equilibrate.sh
	bash equilibrate.sh || exit 1
)

# H-REMD / REST2
# Note: if you don't have at least 12 CPU cores (1 per replica), this will oversubscribe and might be inefficient.
hremd_dir=data/$CMP/$SOLV/hremd-quadratic/$FF
mkdir -p $hremd_dir
cp code/md_templates/hremd-quadratic/* $hremd_dir/ || exit 1
( cd $hremd_dir
	sed -i "s/FORCEFIELD=.*/FORCEFIELD=$FF/;s/SOLVENT_LC=.*/SOLVENT_LC=$SOLV/;s/SOLUTE=.*/SOLUTE=$CMP_NAME/;" 1-get-inputs.sh
	bash 1-get-inputs.sh || exit 1
	bash 2-make-single-topology.sh || exit 1
	bash 3-plumed-prepare-hremd.sh || exit 1
	bash 4-run-local.sh || exit 1
)

After the simulation is done, run make-dry-pdb.sh and then python run-analysis.py --compound COMPOUND --forcefield FORCEFIELD --method METHOD --solvent SOLVENT, with parameters matching the folder naming as explained before.

Re-running the parameterizations

To re-run the parameterization, you can start from SMILES or .mol files.

  • the script code/md_templates/create-initial-structure/smiles-to-structure.py converts a SMILES code to a conformer.
  • the scripts in code/md_templates/parameterize can be used to assign force-field parameters for each force field. Note that for OPLS, the molecule must be manually uploaded to LigParGen (https://zarbi.chem.yale.edu/ligpargen/), and for XFF, the molecule must be uploaded to the XFF web server (https://xff.xtalpi.com/)