Understanding command line

[Sanjay Paul]

Hello everyone, 

I used the following command line for binding energy calculation...as it was present in the example file. 

gmx_MMPBSA -O -i mmpbsa.in -cs md_100.tpr -ci index.ndx -cg 1 13 -ct md_100_center.xtc - cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv  

However, I couldn't understand " -cg 1 13".......are they protein and ligand group numbers in the index file?

Becoz in my index file....number 1 =system and number 13 = other. 

Sequence in index file: 

1. System 2. Protein 3. Protein-H, 4. Calpha 5. Backbone 6.Mainchain 7.Mainchain+Cb 8. Mainchain+H 9. Side chain 10. Sidechain-H 11. Prot-Masses 12. non-Protein 13. Other 14. LIG 15. NA 16. Water 17. Sol 18. Non water 19. Ion 20. Water and ion 21. Protein_LIG

Please suggest me the group number

[Mario Sergio Valdes]

The gromacs index.ndx file indexes (lists) molecules according to their type, nature, selection, etc. It is important to understand Gromacs before venturing into other tools because it can carry errors.
Normally, group 0 (not to be confused with the number in the sequence of elements, which would be the first) is the system that contains all the atoms of all the molecules in the system. If you check the example, you will see that in that case 1 belongs to the group "Protein" and 13 belongs to "LIG" (or 3-letter code of the ligand). In that case, it can be selected like that, because the receptor and the ligand are different. In other examples, you will see that 3 and 4 are used because the index comes from CHARMM-GUI. In that case, the groups must be created manually, because they are both proteins and are contained in the same group. To do this, a selection command in gmx make_ndx is used to separate them (splitch).
The selection of the groups depends on the system and its composition. Probably, if it is Protein-Ligand, you can select 1 and 13 but do not use gmx_MMPBSA as a black box. It is important to have at least a basic understanding of what it does and why it does it. We recommend you download the examples folder and explore, analyze, and understand them so that you can quickly become an expert in gmx_MMPBSA.