Protein-ligand binding free energy calculations with psf_dcd files¶
Info
This example can be found in the examples/psf_dcd/protein_ligand directory in the repository folder. If you didn't use gmx_MMPBSA_test before, use downgit to download the specific folder from gmx_MMPBSA GitHub repository.
In this example we are going to generate gmx_MMPBSA input files from psf_dcd files. It is strongly recommended to check how gmx_MMPBSA works before attempting any sort of calculations. See below the input files required for running gmx_MMPBSA.
Make sure to install gmx_MMPBSA in a dedicated conda environment as decribed here.
Requirements¶
In this case, gmx_MMPBSA requires:
| Input File required | Required | Type | Description |
|---|---|---|---|
| Input parameters file | in | Input file containing all the specifications regarding the type of calculation that is going to be performed | |
| A trajectory file | xtc pdb | Final GROMACS MD trajectory, fitted and with no pbc. | |
| A topology file | top | GROMACS topology file (The * .itp files defined in the topology must be in the same folder | |
| The MD Structure+mass(db) file | pdb | Structure file containing the system coordinates | |
| An index file | ndx | File containing the receptor and ligand in separated groups | |
| Receptor and ligand group | integers | Group numbers in the index files | |
| A Reference Structure file | pdb | Complex reference structure file (without hydrogens) with the desired assignment of chain ID and residue numbers |
-> Must be defined -- -> Optional, but recommended -- -> Optional
Steps to generate gmx_MMPBSA files
The input file *.in is already included in the tutorial folder, although it can be easily generated using --create_input command. The *.in input file, is a text file containing the following lines:
See a detailed list of all the options in gmx_MMPBSA input file here as well as several examples
We are going to use cpptraj program from Amber to process the *.psf and *.dcd files:
Press enter after every command line
cpptraj -p step3_input.psf
>trajin traj.dcd
>strip :POT,CLA,TIP3,SOD
>trajout traj.xtc
>run
>exit
After executing these commands, there should be a new file in te folder, i.e. traj.xtc that is going to be used as the trajectory file.
Keep in mind
For some reason, when using charmm-gui to prepare the files, the toppar files that come inside the NAMD folder have the ATOM section commented with the ! symbol:
!ATOMS
!MASS -1 H 1.00800 ! polar H
!MASS -1 HC 1.00800 ! N-ter H
!MASS -1 HA 1.00800 ! nonpolar H
!MASS -1 HP 1.00800 ! aromatic H
!MASS -1 HB1 1.00800 ! backbone H
!MASS -1 HB2 1.00800 ! aliphatic backbone H, to CT2
!MASS -1 HR1 1.00800 ! his he1, (+) his HG,HD2
...
This section can't be commented on for the purpose of this tutorial, thus you can either use a files with the ATOM section uncommented or just uncomment the section yourself:
We are going to use ParmEd to convert the *.psf file into a GROMACS topology file. To do so, use the ParmEd script that is already included in the tutorial folder.
python script.py
Take your time to analyze step by step the process of converting .psf/.crd files intoa GROMACS topology with ParmEd.
# import ParmEd module
import parmed as pmd
# load psf file
psf = pmd.load_file('step3_input.psf')
#load coordinate file
psf.coordinates = pmd.load_file('step3_input.crd').coordinates
# strip ions and water
psf.strip(':POT, CLA, TIP3, LIT, SOD, RUB, CES, BAR')
# load Charmm Parameter Set. Make sure to include all the necessary force field files in this list
params = pmd.charmm.CharmmParameterSet('toppar/par_all36_carb.prm',
'toppar/par_all36_cgenff.prm',
'toppar/par_all36_lipid.prm',
'toppar/par_all36m_prot.prm',
'toppar/par_all36_na.prm',
'toppar/par_interface.prm',
'toppar/toppar_water_ions.str',
'toppar/ben.prm')
psf.load_parameters(params)
# save GROMACS topology file
psf.save('gromacs.top')
psf.save('gromacs.pdb')
The last file we need to generate is the index file containing the groups with the receptor and ligand atoms. To do so, just use make_ndx from GROMACS and the MD Structure+mass(db) that was generated previously.
Press enter after every command line
gmx make_ndx -f gromacs.pdb -o index.ndx
>q
In this case, there is no need to generate new groups as GROMACS is able to parse the receptor and ligand atoms. The groups number 1 and 13 contain the receptor and the ligand atoms, respectively.
Once the gmx_MMPBSA files have been generated, the program can be run either in serial or in parallel:
gmx_MMPBSA -O -i mmpbsa.in -cs gromacs.pdb -ct traj.xtc -ci index.ndx -cg 1 13 -cp gromacs.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
mpirun -np 2 gmx_MMPBSA -O -i mmpbsa.in -cs gromacs.pdb -ct traj.xtc -ci index.ndx -cg 1 13 -cp gromacs.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
Considerations¶
In this case, a single trajectory (ST) approximation is followed, which means the receptor and ligand structures and trajectories will be obtained from that of the complex. To do so, an MD Structure+mass(db) file (gromacs.pdb), an index file (index.ndx), a trajectory file (traj.xtc), and both the receptor and ligand group numbers in the index file (1 13) are needed. The mmpbsa.in input file will contain all the parameters needed for the MM/PB(GB)SA calculation. In this case, 11 frames are going to be used when performing the MM/PB(GB)SA calculation with the igb5 (GB-OBC2) model and a salt concentration = 0.15M.
A plain text output file with all the statistics (default: FINAL_RESULTS_MMPBSA.dat) and a CSV-format output file containing all energy terms for every frame in every calculation will be saved. The file name in '-eo' flag will be forced to end in [.csv] (FINAL_RESULTS_MMPBSA.csv in this case). This file is only written when specified on the command-line.
Note
Once the calculation is done, the results can be analyzed in gmx_MMPBSA_ana (if -nogui flag was not used in the command-line). Please, check the gmx_MMPBSA_ana section for more information
Created: March 4, 2022 10:09:43