Input files preparation for gmx_MMPBSA

[Dong Man Jang]

I made run MD simulation using Gromacs and obtained trajectories of protein-ligand complex. 

I want to run protein-ligand binding free energy calculation (multiple trajectory method using gmx_MMPBSA), but I am having hard time to prepare input files. 

<From the example tutorial in gmx_MMPBSA site>

 $  gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct com_traj.xtc -rs rec.pdb -ri rec_index.ndx -rg 1 -rt rec_traj.pdb -lm ligand.mol2 -ls lig.pdb -li lig_index.ndx -lg 2 -lt lig_traj.pdb

In this tutorial, as far as I understand, I need to prepare structures, trajectory files of Receptor (-rs rec.pdb -ri rec_index.ndx -rg 1 -rt rec_traj.pdb) and Ligand (-lm ligand.mol2 -ls lig.pdb -li lig_index.ndx -lg 2 -lt lig_traj.pdb) as well as Complex. 

From the MD simulation result of Gromacs, I obtained result files related to complex but I do not have receptors and ligand files (such as rec_traj.pdb, lig_traj.pdb). Is there any easy way to generate these files from the complex trajectories? 

When I search on google, I found that ante-MMPBSA.py is something like generating input files for MMPBSA.py in AMBER. I wonder if there are similar tools or easy ways to prepare input files to run gmx_MMPBSA.

Many thanks!

Dongman Jang

[Mario Ernesto]

Hello there! and welcome :) 

I see there is a little misunderstood here...

you are referring to the multiple trajectory protocol where it's assumed either the receptor or the ligand (or both) have a different "behavior" in the free state compared to the one observed in the bound complex. When using multiple trajectory protocol, you will have to run the MD simulation for the receptor and/or the ligand and use the command you refer to above.

However, if you have only the trajectory for your complex and you assume either the receptor or the ligand (or both) have a similar "behavior" in the free state compared to the one observed in the bound complex, you can use the single trajectory protocol, and omit to give the information for the receptor and/or the ligand as it will be extracted from that of the complex. Check this tutorial for running the single trajectory protocol here:

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/Protein_ligand/ST

hope this helps and don't hesitate to contact us if you have any other questions 

cheers!

Mario E.

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[Dong Man Jang]

Oh I see...

Now I understand, and I successfully run gmx_MMPBSA via single trajectory protocol as you suggested. 

Thank you for your kind and quick response.

Sincerely,

Dongman Jang

 

2021년 7월 1일 목요일 오후 2시 39분 42초 UTC+9에 marioe911116님이 작성: