[Basic question] Using gmx_MMPBSA is it possible to single protein energy calculation ?

[Kyoung Pyo Kwon]

Hello all of my senior :)

i'm beginner of this field.

i have total 3 systems(monomer) (Origin, L194F, L194A) mutant

so i want to calculate intra and inter molecule interaction energy of protein
and then i want to compare the energy of mutants and origin protein

is there any guide or good reference of this ?

Thank you !

[Mario Sergio Valdes]

Welcome! 

Yes. Calculate the energy for each system independently as exemplified in any of our examples (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/). Then you can open all 3 together in gmx_MMPBSA_ana for comparative analysis.
Happy BFE calculation!

[Isaac Silverman]

To calculate an individual protein's energy I see in the documentation for a single trajectory method that this command line is used:

gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ct com_traj.xtc -ci index.ndx -cg 3 4 -cp topol.top

What groups do 3 and 4 correspond to? For me 3 is C-alpha and 4 is Backbone. Are those the correct groups?

Also, where in the documentation could I find how to do comparative analysis of several systems of energy calculations? Does this have to do with the correlation function?

Thank you in advance!

[Mario Sergio Valdes]

To calculate an individual protein's energy I see in the documentation for a single trajectory method that this command line is used:

gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ct com_traj.xtc -ci index.ndx -cg 3 4 -cp topol.top

What groups do 3 and 4 correspond to? For me 3 is C-alpha and 4 is Backbone. Are those the correct groups?

If you look closely at the example and open the index file with gromacs, you will see that these groups correspond to the receptor and ligand, and they are specific to this system. So, you must create the groups according to your system and properly define them in the command line (-cg)

 

Also, where in the documentation could I find how to do comparative analysis of several systems of energy calculations? Does this have to do with the correlation function?

gmx_MMPBSA_ana support opening multiple systems simultaneously. However, there is not a proper implementation of the comparative analysis. We are working on it. So, for now, you only compare them visually and export the data in csv to make more advanced comparisons using external tools. Several articles use gmx_MMPBSA for energy calculation and then are used other tools to compare multiples systems

 

[Isaac Silverman]

So what is the function of the correlation feature? I see in the documentation that it is being worked on. Is it in effect now?

If it is a single trajectory method with only a protein and no ligand, can the energy still be calculated for the single protein? If so, how can I adjust the command line (what groups should be input) to do so?

Thank you

[Mario Sergio Valdes]

So what is the function of the correlation feature? I see in the documentation that it is being worked on. Is it in effect now?

The correlation function is designed to generate a parameterization. That is, from multiple ligands bound to the same receptor or similar protein families, you can generate a parameterization to estimate the energy for new ligands related to the receptor. In simple terms, a specific receptor (or protein family) parameterization. If you consult the literature, you will find that this is most common, since these endpoint methods tend to overestimate the energy.

This feature is working since version v1.6.0, but it doesn't have documentation.

 

If it is a single trajectory method with only a protein and no ligand, can the energy still be calculated for the single protein? If so, how can I adjust the command line (what groups should be input) to do so?

No. gmx_MMPBSA only works for complexes.