What is wrong with my complex

Yes, as I said complex.gro, complex.pdb, and unk files are for a ligand whereas the 6lu7.pdb, 6lu7.pdbqt, out_ligand_1.pdbqt, amentofl…pdb and amentod…pdbqt are for other ligand.
So you just see complex.gro, complex.pdb, and unk files.

Those are all consistent with the ligand bound to the protein. What exactly is the problem? The ligand is not far away from the protein as you’ve been stating. It’s bound.

I tried to open complex.gro with Chimera and ligand was not at all. While when I saw complex.gro in VMD ligand was not as before far away from protein.


Is it a problem at the protein_clean.pdb file that at the startin document is Discovery studio statements as are in picture

I don’t know what that image is supposed to show. REMARK lines are irrelevant.

The ligand is in complex.gro and complex.pdb and it’s in the same place.

I should note that complex.pdb has the ligand as a separate MODEL, which is why it may not show up in some visualization software. That is not an issue in complex.gro.

So, complex.gro file is correct and I can continue in this way.

I just opened complex.gro file that I sent you via VMD, the ligand is not anywhere also with Chimera ligand was not anywhere

Also, should I add all hydrogen to ligand during the complex.pdb preparation and what about missing residues, is it necessarily to check protein.pdbqt for missing residues.

What representation are you using in that VMD view?

It looks like you are using ribbons, which only the protein will appear. Anything that is not a protein will not. So it isn’t surprising you can’t see the ligand. You need to either show all that is in the file using lines, licorice, CPK etc representations, or make a second rep for the ligand, select it specifically, then use licorice, CPK etc to show it.

To confirm to yourself how these file formats work, open it with a text editor, look through it. I suspect that the bound ligand coordinates will be at the end, with the protein first. And if you do, you will see that it is indeed there. Just did that myself, and there it is, marked as being a UNK residue.

I tried once again from beginning and again, at the complex.gro file ligand seems far away from protein. Please see attached files and if you can help me. I know I am disturbing you so much.
As for you comment, I used CPK and also wrote resname UNK (as is in complex) and nothing had.
https://drive.google.com/drive/folders/1LOkTDzN2QSJm3Qr9zuL5f8K5aA10e2RG?usp=sharing

Did you open the file and look at it? One you posted earlier was marked as complex(4).gro and it was in there.

306GLN OE1 4676 -4.351 0.278 3.297
306GLN NE2 4677 -4.369 0.168 3.102
306GLN HE21 4678 -4.328 0.245 3.050
306GLN HE22 4679 -4.397 0.084 3.054
306GLN C 4680 -4.265 -0.155 3.440
306GLN OT1 4681 -4.246 -0.246 3.517
306GLN OT2 4682 -4.354 -0.245 3.490
0UNK O 1 -0.801 1.842 6.912
0UNK O 2 -1.164 1.199 6.929
0UNK O 3 -0.551 1.892 6.777
0UNK O 4 -1.077 1.353 6.582

Can’t access that last link you posted.

https://drive.google.com/drive/folders/1LOkTDzN2QSJm3Qr9zuL5f8K5aA10e2RG?usp=sharing

Now you can access to the link. For the complex.gro file that you will find attached also ligand coordinated are immediately after protein but still ligand is away from protein. see picture

This is something that you can problem solve, and find where the problem is introduced, go through your process step by step. At each step visualise the location of the protein and the ligand (ensure check across the PBC too), and also look at the contents of the coordinate file. At which step does the relative location of the protein and ligand change? You’ve noted above that you’ve tried lots of things to solve the issue you are seeing, so you must have pinned down the step where things are going wrong? With what command or process is that occurring?

If you want to share your process and files you need to make it as easy as possible for others to follow. Label things as step 1, step 2 etc, detail exactly what is done in each step including commands that are copy and pasted, and name the files in the same manner with a descriptive file name e.g.

  • step1_protein.pdb
  • step2_docked_protein_ligand.pdb
  • step3_protein.gro
  • step3_ligand_moved.gro
  • step4_protein_ligand.gro

Dear member,

I followed every single step of protein-ligand tutorial at official gromacs tutorial from Dr. Justin Lemkul.

Based on the fact that preparation of the complex.gro takes little time I attached my original autodock vina results, protein.pdbqt and ligand.pdbqt, in order to be able you to form complex.gro file by yourself, to see if I am making mistakes.

Finally my ligand is in docked position at complex.gro file using Lemkul recommendation but now I am having problem during add ions.

The order of the atoms in the coordinates and topology must be the same.

How can I solve this, just by text editing the solv.gro file?
Also for the first problem, when I went with command gmx editconf -f lig_ini.pdb -o lig.gro again ligand was far from protein while when I went directly gmx editconf -f lig.pdb -o lig.gro ligand was at docked position. Maybe the problem with solv.gro file can be caused becuase of direct way?

Should I replace names of atoms in solv.gro files with names at topol.top?

You can’t just replace the names, the atoms are entirely out of order. Somehow you generated a topology with a ligand coordinate file with the atoms in one order and are now using a different ligand coordinate file to build the complex. You should only ever have one ligand coordinate file that you use that (1) has the docked coordinates and is therefore compatible with the protein coordinates and (2) has the atoms in the same order as the topology.

See above. Deal with one coordinate file that has the coordinates you want. In all the files you’ve shared, it’s a bunch of things with different coordinates that make no sense to me. Simplify :)

Thank you for your answers.