In Restraining the Ligand ligand option is not there

i am running this command but ligand name is not comming
gmx make_ndx -f em.gro -o index.ndx

Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are: 526 Protein residues
There are: 67740 Water residues
There are: 36 Ion residues
Analysing Protein…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…

0 System : 211494 atoms
1 Protein : 8238 atoms
2 Protein-H : 4221 atoms
3 C-alpha : 525 atoms
4 Backbone : 1575 atoms
5 MainChain : 2100 atoms
6 MainChain+Cb : 2587 atoms
7 MainChain+H : 2595 atoms
8 SideChain : 5643 atoms
9 SideChain-H : 2121 atoms
10 Prot-Masses : 8238 atoms
11 non-Protein : 203256 atoms
12 Water : 203220 atoms
13 SOL : 203220 atoms
14 non-Water : 8274 atoms
15 Ion : 36 atoms
16 NA : 36 atoms
17 Water_and_ions : 203256 atoms

even in this command gmx make_ndx -f ligand.gro -o index_ligand.ndx

Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are: 1 Protein residues
Analysing Protein…

0 System : 25 atoms
1 Protein : 25 atoms
2 Protein-H : 13 atoms
3 C-alpha : 0 atoms
4 Backbone : 0 atoms
5 MainChain : 1 atoms
6 MainChain+Cb : 1 atoms
7 MainChain+H : 4 atoms
8 SideChain : 21 atoms
9 SideChain-H : 12 atoms

its reading ligand

You can employ the “make_ndx” tool in Gromacs to establish a group named “LIG” that includes all the ligand atoms. To acquire additional information on this, you can execute “make_ndx -h” or refer to the final lines of the previous runs, located after “17 Water_and_ions: 203256 atoms.”

Second and inconvenient alternative is to manually edit the index file. Simply include “[LIG]” in the index file and add the indexes of all ligand atoms sequentially.

sorry but i am unable to understand what this means can you please tell in detail or easy way

Please look at the GROMACS tutorials for more details: Introduction to molecular dynamics or here.

ok i can edit make_ndx file and write ligand name but then can you please tell me in adding ions step here why ligand is not showing am i doing something wrong when it access topol file

gmx genion -s ions.tpr -o solv_ions.gro -p -pname NA -nname CL -neutral

Reading file ions.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision)
Reading file ions.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision)
Will try to add 36 NA ions and 0 CL ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 211566 elements
Group 1 ( Protein) has 8238 elements
Group 2 ( Protein-H) has 4221 elements
Group 3 ( C-alpha) has 525 elements
Group 4 ( Backbone) has 1575 elements
Group 5 ( MainChain) has 2100 elements
Group 6 ( MainChain+Cb) has 2587 elements
Group 7 ( MainChain+H) has 2595 elements
Group 8 ( SideChain) has 5643 elements
Group 9 ( SideChain-H) has 2121 elements
Group 10 ( Prot-Masses) has 8238 elements
Group 11 ( non-Protein) has 203328 elements
Group 12 ( Water) has 203328 elements
Group 13 ( SOL) has 203328 elements
Group 14 ( non-Water) has 8238 elements

What is the residue name for your ligand? It is being recognized as a Protein residue. So either it is an amino acid or polypeptide, or you have specified the residue name as Protein in residuetypes.dat so it will always be recognized as Protein.

My ligand is serotonin and it is a monoamine then how can i select protein ligand for further use in nvt or npt file

Please answer my first question: what is the residue name for your ligand (serotonin)? I’m specifically asking for the 3-letter code in the coordinate file. If it is SER, then all GROMACS tools expect that it is serine, not serotonin, so you will get this kind of output. Processing the ligand.gro file is correct for generating its restraint file. It doesn’t matter at all if make_ndx claims the residue is Protein for this purpose.

yes, i have given my ligand a 3-letter code as ser thanks for helping me sir
one last question are there any parameter defined for a oxygen molecule or ion in a protein