gmx_mmpbsa Tutorial

Introductions about gmx_mmpbsa

gmx_mmpbsa Tutorial

gmx_mmpbsa is used to calculate the MMPBSA binding energy of the GROMACS trajectory and perform energy decomposition. When calculating, the MM part is completed by the script itself, and the PBSA part is completed by the APBS program. Therefore, before using gmx_mmpbsa, the GROMACS and APBS programs must be installed. The atomic parameters (charge, radius, LJ parameters, etc.) required by gmx_mmpbsa to calculate MM and PBSA come from the .tpr file of GROMACS. Therefore, it is necessary to call the gmx dump program to process the .tpr file in order to extract the required parameters. gmx_mmpbsa also uses the gmx trjconv program to deal with the periodic overlap problem of the trajectory. Of course, you can do this step by yourself without the use of scripts, especially when special processing is required for periodicity.

Tutorials

1. Obtain the input file

  • Generate tpr file, pre-balance
  • Run the finished product simulation to get the xtc trajectory file
  • Generate ndx file, which needs to define three groups: complex (com), protein (pro), ligand (lig). Although the name is pro, lig, it can actually represent any molecule, such as two small organic molecules, and It doesn't have to be protein and ligand.
  • Process the trajectory. If there are dimers, clusters, etc., make sure that there is no separation between the constituent atoms. Other cases can be handled automatically by the script.

gmx_mmpbsa Tutorial

2. Set gmx_mmpbsa calculation parameters

Program path

apbs='c:/apbs1.5/bin/apbs.exe' # APBS: The full path of the APBS executable file. For Linux systems such as:

apbs='/home/users/APBS/bin/apbs'.

Basic parameters

ff=AMBER: Force field type, AMBER, OPLS, CHARMM

trj=1EBZ.xtc: trajectory file

tpr=1EBZ.tpr: tpr file

ndx=index.ndx: index file

com=System: Composite Index Group

pro=Protein: protein index group

lig=BEC: Ligand Index Group

Pointtrj, tpr, ndx, and other variables to the corresponding file, and point com, pro, lig, to the corresponding index group in the index file.

Other parameters are mainly polar parameters, non-polar parameters, and grid parameters used in APBS calculation.

3. Run the script

1. The script first processes the trajectory: 1. Complete; 2. Center and overlap. Then output the configuration to the pdb file.

2. The script extracts the atomic information in the tpr and stores it in the qrv file. It is mainly the charge, radius, LJ parameter and residue information of each atom in the complex.

3. The script obtains the APBS grid parameters according to the coordinates of the atoms in the pdb file, and outputs the configuration of each frame to the pqr file required by APBS, and generates the APBS input file *.apbs. Then calls APBS to calculate the corresponding configuration of each frame apbs file, and calculate the contribution of the polar PB and non-polar SA parts, and then calculate the MM contribution, and carry out the residue decomposition at the same time, and output the result.

* It should be noted that our service is only used for research, not for clinical use.

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