# Mis match bwtween the topol.top and solv.gro file **URL:** \ **Category:** User discussions\ **Tags:** forcefield, grompp, mdrun, installation-error, simulation-setup\ **Created:** [February 18, 2023, 11:27am UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832 "2023-02-18T11:27:58Z")\ **Posts on this page:** 15\ **Page:** 1
**Author:** ![anahhas](https://avatars.discourse-cdn.com/v4/letter/a/d9b06d/32.png) [@anahhas](https://gromacs.bioexcel.eu/u/anahhas)\ **Post date:** [February 18, 2023, 11:27am UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832/1 "2023-02-18T11:27:58Z")
GROMACS version:2021 GROMACS modification: Yes/No Here post your question I got extra number in the topol.top file than solv.gro and this have when I just add solv step. how can i solved it. Thanks, Alaa ---
**Author:** ![anahhas](https://avatars.discourse-cdn.com/v4/letter/a/d9b06d/32.png) [@anahhas](https://gromacs.bioexcel.eu/u/anahhas)\ **Post date:** [February 18, 2023, 9:21pm UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832/2 "2023-02-18T21:21:08Z")
Fatal error: number of coordinates in coordinate file (protein\_ligand\_solv.gro, 61506) does not match topology (topol.top, 80980) ---
**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:** [February 19, 2023, 6:15pm UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832/3 "2023-02-19T18:15:44Z")
The error means you haven’t properly kept track of the contents of the system. Almost all bookkeeping can be done automatically (water and ions), but if you have a ligand as you appear to, you have to make careful manual adjustments to the coordinate and topology files. If one changes, so too must the other. It is not possible to diagnose the origin of this problem without a complete listing of the commands issued to this point and a detailed description of any other manual modifications you have made. Otherwise, it is simply “you haven’t kept track of things properly.” ---
**Author:** ![anahhas](https://avatars.discourse-cdn.com/v4/letter/a/d9b06d/32.png) [@anahhas](https://gromacs.bioexcel.eu/u/anahhas)\ **Post date:** [February 19, 2023, 10:41pm UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832/4 "2023-02-19T22:41:03Z")
The steps as following Parmchk2 –i ligand\_gaff.mol2 –f mol2 –o ligand.frcmod Vi commands.in source leaprc.gaff loadamberparams ligand.frcmod MOL=loadmol2 ligand\_gaff.mol2 check MOL saveamberparm MOL ligand.prmtop ligand.inpcrd Savepdb MOL ligand\_amber.pdb quit tleap -f commands.in acpype -p ligand.prmtop -x ligand.inpcrd -b ligand gmx pdb2gmx -f protein.pdb -o protein.gro -ignh -ter -p protein.top I used OPLS-AA/L I used NH3 and COO- water model: I used #1 that is recommended cat protein.gro ligand\_GMX.gro \> protein\_ligand.gro Vi protein\_ligand.gro and add the number manually of the protein and ligand cp ligand\_GMX.top ligand.itp take the atomtypes from ligand.itp and add it to topol.top under forcfield take the last line of ligand.itp and delete the section of system and ligand add it to topol.top gmx editconf -f protein\_ligand.gro -o protein\_ligand\_box.gro -bt cubic -d 1.0 -c gmx solvate -cp protein\_ligand\_box.gro -cs spc216.gro -p topol.top -o protein\_ligand\_solv.gro download the ions.mdp gmx grompp -f ions.mdp -c protein\_ligand\_solv.gro -p topol.top -o protein\_ligand\_ions.tpr after that the error message appears ---
**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:** [February 20, 2023, 2:59pm UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832/5 "2023-02-20T14:59:02Z")
I cannot identify the source of such a massive disparity; something else must have happened (i.e. you repeated a step somewhere or mismanaged files). I would suggest simply starting over, and at every step, after each command you enter or modification you make, you verify that the topology and coordinates are in sync. Also note that it is inappropriate to generate an AMBER topology for a ligand and try to mix it with the OPLS-AA force field for the protein. You need to use a self-consistent force field for everything, otherwise the results (if you can even get past the syntactical issues) will be nonsensical. ---
**Author:** ![anahhas](https://avatars.discourse-cdn.com/v4/letter/a/d9b06d/32.png) [@anahhas](https://gromacs.bioexcel.eu/u/anahhas)\ **Post date:** [February 20, 2023, 4:13pm UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832/6 "2023-02-20T16:13:02Z")
What is the the commands to generate topology for a ligand using OPLS-AA force field. In case of AMBER forcefield, I used Parmchk2 –i ligand\_gaff.mol2 –f mol2 –o ligand.frcmod Thanks ---
**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:** [February 22, 2023, 4:59pm UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832/7 "2023-02-22T16:59:40Z")
[http://zarbi.chem.yale.edu/ligpargen/](http://zarbi.chem.yale.edu/ligpargen/) ---
**Author:** ![anahhas](https://avatars.discourse-cdn.com/v4/letter/a/d9b06d/32.png) [@anahhas](https://gromacs.bioexcel.eu/u/anahhas)\ **Post date:** [February 27, 2023, 12:00am UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832/8 "2023-02-27T00:00:29Z")
Thank you Still I cann’t solve the proble. I use amber force field and everything goes well until i reach to the add ions The command is gmx grompp -f ions.mdp -c protein\_ligand\_solv.gro -p topol.top -o ions.tpr and the error message is WARNING 17 [file topol.top, line 42]: Atomtype H4 was defined previously (e.g. in the forcefield files), and has now been defined again. This could happen e.g. if you would use a self-contained molecule .itp file that duplicates or replaces the contents of the standard force-field files. You should check the contents of your files and remove such repetition. If you know you should override the previous definition, then you could choose to suppress this warning with -maxwarn. I also attach the topol.top and itp files ![itp](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/05ceb4f52ae5b4bfa02e6150e3d0d9005651f38b.png) [topol.top](https://gromacs.bioexcel.eu/uploads/short-url/48c06uu3LGIobv3mSTdjJMARtbo.top) (833.6 KB) ---
**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:** [March 2, 2023, 2:55pm UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832/9 "2023-03-02T14:55:39Z")
This is your problem: ```auto [atomtypes] ;name bond_type mass charge ptype sigma epsilon Amb N3 N3 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CX CX 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H H 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 HP HP 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 HC HC 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 HA HA 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 N N 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 H1 H1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 NA NA 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CW CW 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 CB CB 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 CN CN 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 C* C* 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H4 H4 0.00000 0.00000 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 O2 O2 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 ``` You are redefining atom types that already exist in the force field. The simple solution is - don’t. If the ligand already uses known atom types, you don’t need to add them in again. ---
**Author:** ![anahhas](https://avatars.discourse-cdn.com/v4/letter/a/d9b06d/32.png) [@anahhas](https://gromacs.bioexcel.eu/u/anahhas)\ **Post date:** [March 5, 2023, 5:39pm UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832/10 "2023-03-05T17:39:25Z")
Thank you. Also, is there any way to make the MD simulation faster since it took 3 days and my computer is on and the work didn’t complete yet ---
**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:** [March 5, 2023, 6:00pm UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832/11 "2023-03-05T18:00:43Z")
MD simulations are computationally expensive. Common laptop or desktop hardware are not suited for running them. You need high-performance computing clusters or specially designed GPU workstations to reasonably run most MD. GROMACS _can_ run on a laptop, but generally speaking, it _shouldn’t_. ---
**Author:** ![anahhas](https://avatars.discourse-cdn.com/v4/letter/a/d9b06d/32.png) [@anahhas](https://gromacs.bioexcel.eu/u/anahhas)\ **Post date:** [March 18, 2023, 9:36pm UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832/12 "2023-03-18T21:36:22Z")
Hello, I transferred all of my files to super computer and I am traying to run the production using this command: gmx\_mpi mdrun -deffnm receptor\_ligand\_prod & Howeverver there is an error message: -bash: gmx\_mpi: command not found How can I solved? Please let me know. Thanks ---
**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:** [March 19, 2023, 2:02am UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832/13 "2023-03-19T02:02:15Z")
You need to speak to your system administrator to understand how to configure your environment. Simply put, the `gmx_mpi` binary is not in your environment’s `$PATH`. How you rectify that depends on the cluster itself, and that’s something an admin can tell you. ---
**Author:** ![anahhas](https://avatars.discourse-cdn.com/v4/letter/a/d9b06d/32.png) [@anahhas](https://gromacs.bioexcel.eu/u/anahhas)\ **Post date:** [March 19, 2023, 10:20pm UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832/14 "2023-03-19T22:20:40Z")
Ok. Will ask them. Thanks a lot ---
**Author:** ![ishika](https://avatars.discourse-cdn.com/v4/letter/i/c37758/32.png) [@ishika](https://gromacs.bioexcel.eu/u/ishika)\ **Post date:** [June 11, 2023, 11:50am UTC](https://gromacs.bioexcel.eu/t/mis-match-bwtween-the-topol-top-and-solv-gro-file/5832/15 "2023-06-11T11:50:21Z")
Sir, I have used swissparam to generate the ligand topology file and I am also facing the same issue. [topol.top](https://gromacs.bioexcel.eu/uploads/short-url/s3VptPPM2L2MDbSwJO6s8AonutD.top) (1.5 KB)