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Hello,
I’m new to this field and want some guidance. I have done docking of a protein and a peptide, and I’d like to perform MD Simulations. Should I take the Protein-Peptide complex post docking as a starting structure and follow the “Protein in solvent” ? Or I should follow the “Protein-Ligand” tutorial?
If the peptide is just made up of the standard amino acids, then just the “Protein in solvent” tutorial for the simulation steps should be fine. For the analysis of the simulation, “Protein-Ligand” is definitely worth taking a look at since it involves analyzing interactions between the 2 molecules.
The “Protein-Ligand” tutorial involves the case where the forcefield doesn’t have the topology information for the ligand before-hand, so it takes you through the process of preparing the novel topology incorporating it into the system topology and temperature-coupling groups, but apart from that, the steps for solvation, minimization, equilibration and production md are basically the same.
Thanks, for the response. Yes, the peptide is made up of standard amino acids, and I was able to do “Protein-Peptide complex” MD Simulation following “Protein in water” tutorial without any issues.
But when I tried “Protein-Ligand” tutorial there were many issues that I came across. When I have treated “peptide” as “ligand” in this case.
I used pdb2gmx to generate topology files for both protein and peptide. And there were confusions while editing topol.top file. And following steps were messed up…
Since, “Peptide” is also considered as “Protein” by gromacs. Is there a way to distinguish between these two groups “Protein” and “Peptide”? I’m unable to visualise protein and peptide separately, like when I type “protein” in “Selected Atoms” in VMD that shows “protein + peptide”.
In order to create new groups of atoms which aren’t automatically recognized, you can create an index file listing atoms in the additional groups you want to use, then specifying that file in subsequent commands. You can use gmx make_ndx to create a new index file where the peptide is defined as its own group (you can check which atom numbers correspond to the peptide by looking in the .gro file and then specifying those atoms in their own group), and for the commands which need that distinction, you can specify the index file with -n index.ndx.
To be clear, when I mentioned using the “Protein-Ligand” tutorial for the analysis of the simulation, I meant skipping to the analysis section of that tutorial and apply it to the simulation of the protein-peptide you’d already run with “Protein in water”, running a whole new simulation using that tutorial would just be redundant
Thanks again. I have taken a .gro file and wanted to make groups using the command as you suggested it gave options to pick from, there is option “1 Protein” with 2061 atoms out of which 101 atoms belongs to peptide and rest is protein. OR in terms of residues there are 135 residues out of which 6 belongs to peptide and rest is protein.
So the question is how to split the option “1 Protein” into protein and peptide?
Below is attached snapshots for reference the highlighted portion is peptide from a .gro file.
You can enter ‘h’ to find the options for how to specify the atoms, rename the groups, etc. In this case, entering ‘a 1961 - 1988’ should select the atoms you highlighted. If you then open the resulting index.ndx file and scroll to the bottom, you should find the group you made.
Thank you so much, Karis, for clearing my doubts.
