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CHARMM and MM(PB/GB)SA

PB model is recommended when working with CHARMMff files. Nevertheless, the combination of PB/GB models and CHARMM force field hasn't been tested extensively. Please, check this thread for more information and proceed with caution.

Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder494 inhibitor binding free energy calculations (Single Trajectory method) with CHARMMff files

Info

This example can be found in the examples/COVID-19_related_proteins/Papain-like_protease_7koj 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.

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
The MD Structure+mass(db) file tpr pdb Structure file containing the system coordinates
Receptor and ligand group integers Receptor and ligand group numbers in the index file
A trajectory file xtc pdb trr final GROMACS MD trajectory, fitted and with no pbc.
A topology file top take into account that *.itp files belonging to the topology file should be also present in the folder
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

See a detailed list of all the flags in gmx_MMPBSA command line here

Command-line

That being said, once you are in the folder containing all files, the command-line will be as follows:

gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 18 13 -ct com_traj.xtc -cp topol.top

mpirun -np 2 gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 18 13 -ct com_traj.xtc -cp topol.top

where the mmpbsa.in input file, is a text file containing the following lines:

Sample input file for PB calculation
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Sample input file for PB calculation
This input file is meant to show only that gmx_MMPBSA works. Althought,
we tried to used the input files as recommended in the Amber manual,
some parameters have been changed to perform more expensive calculations
in a reasonable amount of time. Feel free to change the parameters 
according to what is better for your system.

&general
sys_name="SARS_CoV2_Papain_like_protease",
/
&pb
#radiopt=0 is recommended which means using radii from the prmtop file for both the PB calculation and for the NP calculation
istrng=0.15, fillratio=4.0, radiopt=0, inp=1,
/

Remember

radiopt = 0 is recommended which means using radii from the prmtop file

See a detailed list of all the options in gmx_MMPBSA input file here as well as several examples

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 (com.tpr), an index file (index.ndx), a trajectory file (com_traj.xtc), and both the receptor and ligand group numbers in the index file (18 13) are needed. The mmpbsa.in input file will contain all the parameters needed for the MM/PB(GB)SA calculation. A topology file is also needed (mandatory) in this case to generate the topology files in amber format with all the terms for CHARMM force field.

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

Last update: 2023-06-24
Created: 2023-06-24