bieniekmateusz / fegrow-case-sarscov2-3toR

RBFE input files for the reproduction of the study case sarscov2-3toR in rgroup package.

rgroup-case-sarscov2-3toR

RBFE input files for the reproduction of the study case sarscov2-3toR in the rgroup package.

BioSimSpace protocols and scripts used to generate the input files for FEP calculations.

The following details the procedure for protein-ligand binding free energy calculations.

File Setup for Free Energy Calculations

Install BioSimSpace (https://github.com/michellab/BioSimSpace/)

1a) Parameterise the protein with AMBER forcefield:

• Given the protein in pdb format, use the parameterise.py script from BioSimSpace to parameterise it with the ff14SB amber forcefield, and generating .rst7 and .prm7 files: parameterise.py --input FILE.pdb --forcefield ff14SB --output FILE
• save the generated .rst7 and .prm files in the 1.prot_param directory

1b) Generate AMBER format forcefield for the ligands (GAFF):

• Given a molecule in a pdb format in lig_0_initial_pdb directory, use parameterise.py --input MOL.pdb --forcefield GAFF2 --output MOL
• Save each molecule's .rst7 and .prm in lig_1_params

2) Combine each ligand and protein:

• for each ligand, combine it with the protein: combine.py --system1 MOL.prm7 MOL.rst7 --system2 PROTEIN.prm7 PROTEIN.rst7 --output PROT_MOL in the com_0_params directory
• this will create unsolvated prm7 and rst7 files

3a) Solvate the ligands:

• solvate each of the ligand files with solvate.py --input MOL.prm7 MOL.rst7 --output MOL_sol --water tip3p --box_dim 35 in the lig_2_soleq
• --box_dim is the box size used for our system in Angstroms

3b) Solvate the complex:

• solvate the prm7 and rst7 files of the complxes: solvate.py --input PROT_MOL.prm7 PROT_MOL.rst7 --output PROT_MOL_sol --water tip3p --box_dim 90 in the com_1_soleq directory
• --box_dim is the box size used for our system in Angstroms

4) Equilibrate the solvated systems:

   WARNING: Equilibration should be used after generating the FEP files which decide on which atoms will be morphed in each transformation. Otherwise, some of the morphing atoms across the two RBFE legs might not be the same. Here we used a workaround. Please see our updated protocols or aply equilibration after FEP preparation. 

• equilibrate the _sol.rst7 files for the bound and unbound systems (e.g. mol_sol_eq.rst7 or prot_mol_sol_eq.rst7): amberequilibration.py --input MOL_sol.prm7 MOL_sol.rst7 --output MOL_soleq in both lig_2_soleq and com_1_soleq directories. Note the new suffix _soleq.

5) Generate the files for the free energy calculations:

• create the perturbation files for the free energy calculations (e.g. for a transition of Lig1 to Lig2 the above command will create .mapping, .mergeat0.pdb. .pert, .prm7 and .rst7 files for this pertubration). Use this command for both bound and unbound environments: prepareFEP.py --input1 PROT_MOL_soleq.prm7 PROT_MOL_soleq.rst7 --input2 PROT_MOL_soleq.prm7 PROT_MOL_soleq.rst7 --output PROT_MOL1_to_MOL2 in the com_2_fep directory.
• In order to ensure that the same perturbation is used for both of the RBFE legs, modify the prepareFEP.py script to load the mapping from the complex, and then use it in the lig_3_fep. See the warning above to avoid this workaround.

6) Free Energy Calculations

Copy the directory Parameters and the scripts complex_lambdarun-comb.sh and ligand_lambdarun-comb.sh into the main directory. The Parameters folder contains the main configuration file lambda.cfg.

For each transformation:

1. Create a directory named MOL1-MOL2. In the directory run python ../init.py to initialise the directory.
2. The lambda.cfg file contains various parameters, namely the number of moves and cycles, the timestep, the type of constraints, the lambda windows used and the platform on which to run the calculation.
3. Run the ligand_lambdarun-comb.sh and complex_lambdarun-comb.sh scripts

• Script ligand_lambdarun-comb.sh runs the command for the unbound perturbations, whilst complex_lambdarun-comb.sh runs the bound perturbations.

4. Gather the results by runing analyse_freenrg mbar -i lambda-*/simfile.dat -o out.dat -p 90 in all discharge and vanish directories.

Results

In addition to the above instructions for generating the input files for this paper, the results directory also contains the raw data (free energy calculations) which can be analysed with python run_networkanalysis.py sars/sarscov2-3toR.csv --target_compound 14 -o sars.dat -e sars/sarscov2_ic50_exp.csv --stats --generate_notebook.

This protocol was carried out in both forward and backward directories counting effectively as two replicas.