What is wrong with my complex

GROMACS version:2020.2
I did simulation gromacs 10ns, but now after simulation I opened complex file before simulation and I see that my ligand is not in docked position as it should be. I wanted to compare simulated pdb with complex pdb.
Is there anything wrong with complex preparation in the beginning of complex or what is the matter?
complex simulaiot

I followed protein-ligand gromacs tutorial


Dea Sir,
Could you please tell exactly what I need to do in order to eliminate this issue.

Use gmx trjconv to make molecule whole.

gmx trjconv -f .gro/.trr -s *tpr -pbc whole

Also familiarize yourself with periodic boundary conditions

Bit further down the link that I provided … http://manual.gromacs.org/documentation/current/user-guide/terminology.html#suggested-workflow

You will need to try and see what works with your system, as it can be highly variable. I would try first making molecules whole, then centering your system on a molecule or residue (the ligand might be the best option).

Dear Gromacs experts,

I still have not found a solution for my problem, it looks messed.
In complex.pdb is also the ligand far away from protein same as complex.gro

Based on the files you sent me on ResearchGate, the initial coordinates are wrong as the ligand is not in the active site to start with. Correct that and start your simulation from a proper complex.

Dear Gromacs experts,

I am having again problems with complex.gro file, the ligand is far away from protein. I tried hundred ways but did not solve my problem. I used autodock vina for docking, I build complex.pdb like this: I open DIscovery studio, open protein.pdbqt then dragg our_conf_1.pdbqt and save as pdb file. Then through gromacs I separate ligand and protein. If there is anyone who can help I would be able to share my files, just to be helped.


  1. Separate the protein and ligand from the original docked complex (assumes “LIG” is the ligand name, just substitute whatever it really is):
grep -v LIG complex.pdb > protein.pdb
  1. Save the ligand coordinates (assumes it has all the H atoms you need, if not, you need to build those on in some modeling software and ensure it does not alter the non-H coordinates):
grep LIG complex.pdb > lig.pdb
  1. Generate ligand topology with whatever tools are available for the force field you’ve chosen to use.

  2. Run pdb2gmx on the protein:

gmx pdb2gmx -f protein.pdb -o protein_processed.gro
  1. Change coordinate format for the ligand. Strictly speaking, this isn’t necessary (you can use PDB format) but if any H were built on to the protein via pdb2gmx this may be easier:
gmx editconf -f lig.pdb -o lig.gro
  1. Copy and paste the coordinates of lig.gro into protein.gro and save as complex.gro. Update the number of atoms in the second line of complex.gro.

  2. Proceed as normal with positioning the complex within a box, solvate, etc.

Visually verify the correctness of the coordinates after every step. If something is amiss, you know what has gone wrong rather than trying “hundreds of ways.”

Also, if you haven’t done it already, run through this tutorial: http://www.mdtutorials.com/gmx/complex/index.html

I tried, but having problem with separated ligand (picture attached).
For docking I used autodock vina, docked complex I prepared: Opening protein.pdbqt in pymol and then opening out_ligand_1.pdbqt, adding hydrogens to ligand and thenUntitled save as pdb file.

OK, so you’re starting from incorrect coordinates. You need to solve the issue regarding PDBQT -> PDB conversion. PDB is a fixed-column format, and my guess is that your conversion/export feature is violating the required column alignment.

Yeah, the problem is in pdb docked complex preparation. But I don`t know how to prepare properly, I tried using DS, PyMOL and Moe, but wrong. Maybe if I can send you pdbqt files (protein and ligand) would be a good idea.

Open the protein and ligand PDB files and see if the columns line up. I suspect they don’t. It’s simple to fix in a text editor. If you need help doing that, attach the files to your post here.

Since here it is not possible to attach pdb, pdbqt files, I will send you at researchgate. Also please find attached complex.gro file that I build exactly as you recommended, when I opened to visualize the ligand was not there.

Please upload to Google Drive, etc. I do not want to have part of the conversation privately and the other publicly via this forum. The purpose of this forum is not just for you to get your problem solved but for others to learn from the discussion.


unk files and complex.gro, complex.pdb are for one ligand tha I tried MD
Wherease other files are autodock vina results for preparing compelx files

The ligand coordinates from out_ligand_1.pdbqt and complex.pdb are completely different, so however you’re extracting the initial coordinates is not giving you the same ligand position as you’re likely expecting. I know very little about ADT/AutoDock but your problem lies there. Both complex.pdb and complex.gro have the same coordinates and the ligand is bound to the protein. If it’s not where it should be, then your export from ADT is what’s going wrong. You should seek help with using those tools on whatever help forum ADT offers.