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…
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.
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
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.
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