Skip to content

Alanine scanning

Info

This example can be found in the examples/Alanine_scanning 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
An index file ndx file containing the receptor and ligand in separated groups
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 (not included) top GROMACS topology file (The * .itp files defined in the topology must be in the same 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 20 21 -ct com_traj.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
mpirun -np 2 gmx_MMPBSA MPI -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 20 21 -ct com_traj.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
gmx_MMPBSA_test -t 12

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

Sample input file for Alanine scanning
Sample input file for Alanine scanning
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="Alanine_Scanning",
startframe=1,
endframe=10,
forcefields="leaprc.protein.ff14SB", 
PBRadii=4,
/
&gb
igb=8, saltcon=0.150,
/
&alanine_scanning
mutant='ALA', mutant_res='A:23', cas_intdiel=1
/

Keep in mind

See a detailed list of all the options in gmx_MMPBSA input file here as well as several examples. These examples are meant only to show that gmx_MMPBSA works. It is recommended to go over these variables, even the ones that are not included in this input file but are available for the calculation that it's performed and see the values they can take (check the input file section). This will allow you to tackle a number of potential problems or simply use fancier approximations in your calculations.

Considerations

In this case, a single trajectory (ST) approximation is followed, which means the receptor and ligand amber format topologies 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 (20 21) are needed. The mmpbsa.in input file will contain all the parameters needed for the MM/PB(GB)SA calculation. In this case, 10 frames are going to be used when performing the MM/PB(GB)SA calculation with the igb8 (GB-Neck2) model and a salt concentration = 0.15M. Of note, mbondi3 radii (PBRadii=4) will be used as recommended for GB-Neck2 solvation model. Also, The dielectric constant (intdiel) will be modified depending on the nature of the residue to be mutated as cas_intdiel=1. In this case, the residue A/23 is a Tyrosine which means intdiel = 3 will be used.

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

How to define properly which residue is going to be mutated?

The generated PDB files must keep the original numbering, so selection based on residue number is reliable. However, the chain id can vary depending on several factors. If you use the reference structure (-cr flag), then you don't have to worry about any changes. The selection will be based on this structure.

On the other hand, if this reference structure is omitted, then it will depend on:

  • GROMACS version

    We have noticed that in GROMACS 20xx.x versions, trjconv can omit the chain IDs.

  • The option assign_chainID

    This option defines when chain IDs are assigned. Please see this variable in &general namelist variables section

Tip

In any of these cases, you must verify that the selection is correct. You can see the structure of the fixed Complex structure (_GMXMMPBSA_FIXED_COM.pdb), Receptor (_GMXMMPBSA_REC_Fx.pdb), and ligand (_GMXMMPBSA_LIG_Fy.pdb) respectively. x and y represent the fragment for discontinuous molecules


Last update: June 11, 2022 23:23:12
Created: February 8, 2021 07:10:13
Back to top