# Protein-Ligand complex MD simulation **URL:** \ **Category:** User discussions\ **Created:** [July 26, 2023, 7:16pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-md-simulation/6894 "2023-07-26T19:16:32Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![isilver](https://avatars.discourse-cdn.com/v4/letter/i/13edae/32.png) [@isilver](https://gromacs.bioexcel.eu/u/isilver)\ **Post date:** [July 26, 2023, 7:16pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-md-simulation/6894/1 "2023-07-26T19:16:32Z")
GROMACS version: 2020 GROMACS modification: Yes/No Here post your question I have been attempting to do a Protein-Ligand simulation and ran into an error. I converted the pdb file of the protein to generate a .gro file, a itp (posre) file, and a topol.top file. I used LigParGen to create the .itp and .gro file for the ligand. When I attempted to structure the topol.top file to include the Ligands files I ran into an error when trying to add ions to the box. The error read as follows ERROR 1 [file topol.top, line 28656]: Atomtype opls\_800 not found There was 1 note * * * Program: gmx grompp, version 2020 Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1408) Fatal error: There was 1 error in input file(s) ## For more information and tips for troubleshooting, please check the GROMACS website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors) The following is the line noted in the error (28656). Additionally I am adding a few lines above the errored line. That was where I added the Posre file for the Protein. The line which was flagged for the error is the list line below. ; Include Position restraint file #ifdef POSRES1 #include “posre.itp” #endif [moleculetype] ; Name nrexcl GTP 3 [atoms] ; nr type resnr residue atom cgnr charge mass 1 opls\_800 1 UNK P00 1 2.7088 30.9738 It appears to be an error with the residue identification. I used LigParGen’s OPLS/CM1A Parameter Generator for Organic Ligands to get the ligand but I keep on getting this error. Do you know why I am running into this error and what I can do to fix it? ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [July 27, 2023, 7:06am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-md-simulation/6894/2 "2023-07-27T07:06:45Z")
When you generated the .itp file, there should be a section labeled atomtypes defining each atom that needs to be called before any residues are defined. You can call them with the #include command, make sure they appear before any moleculetypes are defined ---
**Author:** ![isilver](https://avatars.discourse-cdn.com/v4/letter/i/13edae/32.png) [@isilver](https://gromacs.bioexcel.eu/u/isilver)\ **Post date:** [July 31, 2023, 4:27pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-md-simulation/6894/3 "2023-07-31T16:27:10Z")
what do you mean by call? Should I rename them? This is what my atomtype looks like now- [atomtypes] opls\_808 O808 15.9990 0.000 A 2.96000E-01 8.78640E-01 opls\_823 N823 14.0070 0.000 A 3.25000E-01 7.11280E-01 opls\_825 N825 14.0070 0.000 A 3.25000E-01 7.11280E-01 opls\_832 H832 1.0080 0.000 A 0.00000E+00 0.00000E+00 opls\_806 O806 15.9990 0.000 A 2.90000E-01 5.85760E-01 After that comes the molecule type which reads as follows- [moleculetype] ; Name nrexcl GTP 3 [atoms] ; nr type resnr residue atom cgnr charge mass 1 opls\_800 1 UNK P00 1 2.7088 30.9738 2 opls\_801 1 UNK O01 1 -1.1224 15.9990 3 opls\_802 1 UNK O02 1 -0.9331 15.9990 4 opls\_803 1 UNK H03 1 0.4396 1.0080 5 opls\_804 1 UNK O04 1 -0.8933 15.9990 6 opls\_805 1 UNK H05 1 0.4334 1.0080 It appears that the issue is with the lack of residue names and type. How do I generate the names for the residues and the atom type so that gromacs can recognize it? ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [August 1, 2023, 4:29am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-md-simulation/6894/4 "2023-08-01T04:29:39Z")
By call, I mean the topol.top file will use the parameters provided by the .itp files through the #include command. The [atomtypes] defines the atoms and the [moleculetype] and [atoms] uses those atoms to define whatever residue you’re working with. All [atomtypes] must be included (either in an .itp file or in topol.top itself) before any residues can be defined. Was the water topology included before or after your [atomtypes] (should look something like #include ‘…/tip3p’, or whichever water model you’re using)? Could you make sure that the [atomtypes] is included before the water topology is called (the water topology file likely includes a [moleculetype] section for the water model, so you need to make sure your [atomtypes] are listed before the water model), and also make sure UNK is listed as GTP or vice versa (just so the residue name under [moleculetype] and [atoms] match)? ---
**Author:** ![isilver](https://avatars.discourse-cdn.com/v4/letter/i/13edae/32.png) [@isilver](https://gromacs.bioexcel.eu/u/isilver)\ **Post date:** [August 1, 2023, 4:18pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-md-simulation/6894/5 "2023-08-01T16:18:07Z")
Thank you for your response. You were right, I was missing the atomtype before the moleculetype. ---
**Author:** ![juhi.khurana03](https://avatars.discourse-cdn.com/v4/letter/j/57b2e6/32.png) [@juhi.khurana03](https://gromacs.bioexcel.eu/u/juhi.khurana03)\ **Post date:** [October 31, 2023, 4:24am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-md-simulation/6894/6 "2023-10-31T04:24:14Z")
Hello all, I am new to Gromacs. I ran MD simulation for apo protein successfully. But I am facing a lot of issues while running simulation for protein-ligand complex. I have installed the gromacs 2023 version and chramm force field 2022 version. While applying the terminus type, I am getting fatal error for C-terminus type. Any suggestions and help will be highly appreciated. Thank you in advance. ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [October 31, 2023, 8:29am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-md-simulation/6894/7 "2023-10-31T08:29:45Z")
Hello, could you post the exact command you used and copy-paste all the messages that were output into the terminal/output file when you ran the command (so all the notes, warnings and error messages)? Also, could you make a new post for this, just so this one post doesn’t get cluttered with unrelated replies? ---
**Author:** ![dlakhan](https://avatars.discourse-cdn.com/v4/letter/d/ecc23a/32.png) [@dlakhan](https://gromacs.bioexcel.eu/u/dlakhan)\ **Post date:** [June 18, 2024, 1:50am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-md-simulation/6894/8 "2024-06-18T01:50:03Z")
Hello, my name is Dharati Now I am working on GROMACS for only protein and tried to generate topology file with amber force field but it is showing this type of error Fatal error: The residues in the chain LYS1–LEU129 do not have a consistent type. The first residue has type ‘Protein’, while residue ALA9 is of type ‘Other’. Either there is a mistake in your chain, or it includes nonstandard residue names that have not yet been added to the residuetypes.dat file in the GROMACS library directory. If there are other molecules such as ligands, they should not have the same chain ID as the adjacent protein chain since it’s a separate molecule. So, if you know then can you help me to solve this error???