[gmx-users] How to mearg Ligand protein and Lipid

[neha bharti]

Hello All

I am trying to perform MD for protein ligand protein complex in popc lipid
with
charmm36 force field and also follow Justin A. Lemkul tutorial.

I also wanted to ask that while create special index groups consisting of
solvent + ions and protein + lipids using make_ndx if i am having a system
with ligand molecule also then should I add it with protein lipid complex
or add it separately with protein like

16 | 14" to merge the SOL and CL groups

"1 | 13 |" to merge Protein and POPC groups

and
1 | 12 to merge Protein and LIGAND groups

or I can add them like 1 | 12 | 13 to merge Protein and LIGAND and POPC
groups

With Regards
Neha bharty