Ok, then as Justin said: delete the LIG atoms from the pdb file that you use in pdb2gmx and it should work. You obtain a gro-file as result. This gro-file is then combined with the ligand’s gro-file as shown in the tutorial.
Not entirely sure about the TER, but I think pdb2gmx recognizes the termini automatically and you don’t have to worry about the TER (I THINK - I may be wrong here, so just put TER back in and see if it makes any difference)
Your grep command does not remove the ligand coordinates from the protein coordinates. Again, refer to my tutorial which deals with this explicitly using grep -v to generate the protein PDB file that you need.
The error is solved. Thank you.
Dear Sir,
I have performed a protein-ligand simulation using GROMACS Tutorial: Protein-Ligand Complex.
I wan to learn how to do analysis. I have used this command for the calculation of RMSD : gmx rms -s em.tpr -f md_0_10_center.xtc -n index.ndx -tu ns -o rmsd_jz4.xvg
choosing “Backbone” for least-squares fitting and “LIG_Heavy” for the RMSD calculation.
I have attached my graph.
How to know that the calculated RMSD is about 0.1 nm (1 Å) ?
By looking at the graph i feel, that the ligand was stable for the first 10ns simulation, and later till 42ns was very unstable (showed a lot of fluctuations) and after that towards 50ns, it got stable.
Is it a good sign to proceed? how to analyze? Kindly help.
Did you watch the trajectory to see what the protein was actually doing? Always a good idea to actually look at the trajectory and see what is going on. Then you will be able to see if the RMSD jumping from 0.5 to 6nm is reasonable/representative or not.
Upon visualizing the trajectory, I saw that ligand goes out of the system at one point. what does that mean ?
Probably a PBC issue. Re-image with trjconv.
Hi Sanah, I’ve been following the same tutorial as you, I did a 20ns simulation but my RMSD stayed between 0,3 and 0,45nm during the entire simulation. I’m curious what might have caused this difference. Do you mind saying what version of CHARMM36 and cgenff_charmm2gmx.py" conversion script did u use?
Also, did your ligand topology file (jz4.str) looked like the one they show on the tutorial? Cause mine was a bit different, maybe because I’m using newer versions of AVOGRADO and CGenFF server, but I’m not sure.
Hello, I want to simulate DNA that is covalently bonded to a ligand. Should I parameterize the ligand and DNA separately and then merge them together? In this case, might I lose a covalent bond between the DNA and the ligand? Could you please kindly guide me on how I can simulate the DNA covalently bonded to a ligand?
