# What is wrong with my complex **URL:** \ **Category:** User discussions\ **Created:** [July 21, 2020, 9:17pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551 "2020-07-21T21:17:57Z")\ **Posts on this page:** 20\ **Page:** 2
**Author:** ![kastriotademi](https://avatars.discourse-cdn.com/v4/letter/k/5fc32e/32.png) [@kastriotademi](https://gromacs.bioexcel.eu/u/kastriotademi)\ **Post date:** [August 12, 2020, 7:55pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/21 "2020-08-12T19:55:28Z")
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. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [August 12, 2020, 8:08pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/22 "2020-08-12T20:08:00Z")
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. ---
**Author:** ![kastriotademi](https://avatars.discourse-cdn.com/v4/letter/k/5fc32e/32.png) [@kastriotademi](https://gromacs.bioexcel.eu/u/kastriotademi)\ **Post date:** [August 12, 2020, 8:21pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/23 "2020-08-12T20:21:45Z")
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. ![Screenshot from 2020-08-12 21-42-24](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/99cfd2f337340169706702ac84a18b5d16a2cd42.png) Is it a problem at the protein\_clean.pdb file that at the startin document is Discovery studio statements as are in picture ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [August 12, 2020, 8:35pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/24 "2020-08-12T20:35:50Z")
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. ![vmdscene](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/cf99e0da1dda5717998240520d79e77636d1ab98.png) ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [August 12, 2020, 8:38pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/25 "2020-08-12T20:38:28Z")
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. ---
**Author:** ![kastriotademi](https://avatars.discourse-cdn.com/v4/letter/k/5fc32e/32.png) [@kastriotademi](https://gromacs.bioexcel.eu/u/kastriotademi)\ **Post date:** [August 12, 2020, 8:42pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/26 "2020-08-12T20:42:43Z")
So, complex.gro file is correct and I can continue in this way. ---
**Author:** ![kastriotademi](https://avatars.discourse-cdn.com/v4/letter/k/5fc32e/32.png) [@kastriotademi](https://gromacs.bioexcel.eu/u/kastriotademi)\ **Post date:** [August 12, 2020, 8:46pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/27 "2020-08-12T20:46:38Z")
I just opened complex.gro file that I sent you via VMD, the ligand is not anywhere also with Chimera ligand was not anywhere ![Screenshot from 2020-08-12 23-45-29](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/856e3d59f36bfcce8824e3f2514305ce82d7dc74.png) ---
**Author:** ![kastriotademi](https://avatars.discourse-cdn.com/v4/letter/k/5fc32e/32.png) [@kastriotademi](https://gromacs.bioexcel.eu/u/kastriotademi)\ **Post date:** [August 12, 2020, 9:08pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/28 "2020-08-12T21:08:08Z")
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. ---
**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\ **Post date:** [August 12, 2020, 11:30pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/29 "2020-08-12T23:30:21Z")
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. ---
**Author:** ![kastriotademi](https://avatars.discourse-cdn.com/v4/letter/k/5fc32e/32.png) [@kastriotademi](https://gromacs.bioexcel.eu/u/kastriotademi)\ **Post date:** [August 12, 2020, 11:39pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/30 "2020-08-12T23:39:08Z")
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](https://drive.google.com/drive/folders/1LOkTDzN2QSJm3Qr9zuL5f8K5aA10e2RG?usp=sharing) ---
**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\ **Post date:** [August 12, 2020, 11:42pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/31 "2020-08-12T23:42:39Z")
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. ---
**Author:** ![kastriotademi](https://avatars.discourse-cdn.com/v4/letter/k/5fc32e/32.png) [@kastriotademi](https://gromacs.bioexcel.eu/u/kastriotademi)\ **Post date:** [August 13, 2020, 12:00am UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/32 "2020-08-13T00:00:25Z")
[https://drive.google.com/drive/folders/1LOkTDzN2QSJm3Qr9zuL5f8K5aA10e2RG?usp=sharing](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 ![Screenshot from 2020-08-13 02-58-10](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/5e9d0d712208b6b0776256c67cee1cc11769f8cf.png) ---
**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\ **Post date:** [August 13, 2020, 4:00am UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/33 "2020-08-13T04:00:30Z")
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 ---
**Author:** ![kastriotademi](https://avatars.discourse-cdn.com/v4/letter/k/5fc32e/32.png) [@kastriotademi](https://gromacs.bioexcel.eu/u/kastriotademi)\ **Post date:** [August 13, 2020, 8:00am UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/34 "2020-08-13T08:00:14Z")
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. ---
**Author:** ![kastriotademi](https://avatars.discourse-cdn.com/v4/letter/k/5fc32e/32.png) [@kastriotademi](https://gromacs.bioexcel.eu/u/kastriotademi)\ **Post date:** [August 13, 2020, 1:44pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/35 "2020-08-13T13:44:10Z")
Finally my ligand is in docked position at complex.gro file using Lemkul recommendation but now I am having problem during add ions. ![Screenshot from 2020-08-13 16-42-03](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/9afeefa94cd343a58ea38a6d4ad007bc712396a6.png) ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [August 13, 2020, 1:55pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/36 "2020-08-13T13:55:06Z")
The order of the atoms in the coordinates and topology must be the same. ---
**Author:** ![kastriotademi](https://avatars.discourse-cdn.com/v4/letter/k/5fc32e/32.png) [@kastriotademi](https://gromacs.bioexcel.eu/u/kastriotademi)\ **Post date:** [August 13, 2020, 1:59pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/37 "2020-08-13T13:59:34Z")
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? ---
**Author:** ![kastriotademi](https://avatars.discourse-cdn.com/v4/letter/k/5fc32e/32.png) [@kastriotademi](https://gromacs.bioexcel.eu/u/kastriotademi)\ **Post date:** [August 13, 2020, 2:05pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/38 "2020-08-13T14:05:32Z")
Should I replace names of atoms in solv.gro files with names at topol.top? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [August 13, 2020, 2:27pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/39 "2020-08-13T14:27:17Z")
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. > [@kastriotademi](#): > > 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. 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 :) ---
**Author:** ![kastriotademi](https://avatars.discourse-cdn.com/v4/letter/k/5fc32e/32.png) [@kastriotademi](https://gromacs.bioexcel.eu/u/kastriotademi)\ **Post date:** [August 13, 2020, 2:54pm UTC](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551/40 "2020-08-13T14:54:44Z")
Thank you for your answers. [Previous page](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551.md?page=1) [Next page](https://gromacs.bioexcel.eu/t/what-is-wrong-with-my-complex/551.md?page=3)