# Error at grommp for ions.tpr **URL:** \ **Category:** User discussions\ **Created:** [August 16, 2020, 6:51am UTC](https://gromacs.bioexcel.eu/t/error-at-grommp-for-ions-tpr/671 "2020-08-16T06:51:22Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![mayank](https://avatars.discourse-cdn.com/v4/letter/m/bc8723/32.png) [@mayank](https://gromacs.bioexcel.eu/u/mayank)\ **Post date:** [August 16, 2020, 6:51am UTC](https://gromacs.bioexcel.eu/t/error-at-grommp-for-ions-tpr/671/1 "2020-08-16T06:51:22Z")
GROMACS version: 2020.1 GROMACS modification: No I was trying to prepare a system using dimethyl-sulfoxide as a solvent in oplsff after solvation step i am getting this error:- Command line: gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1 Ignoring obsolete mdp entry ‘title’ Ignoring obsolete mdp entry ‘ns\_type’ NOTE 1 [file em.mdp]: With Verlet lists the optimal nstlist is \>= 10, with GPUs \>= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to -717712930 Generated 330891 of the 330891 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 330891 of the 330891 1-4 parameter combinations ERROR 1 [file dmso.itp, line 75]: No default Ryckaert-Bell. types ERROR 2 [file dmso.itp, line 76]: No default Ryckaert-Bell. types ERROR 3 [file dmso.itp, line 77]: No default Ryckaert-Bell. types ERROR 4 [file dmso.itp, line 78]: No default Ryckaert-Bell. types ERROR 5 [file dmso.itp, line 79]: No default Ryckaert-Bell. types ERROR 6 [file dmso.itp, line 80]: No default Ryckaert-Bell. types ERROR 7 [file dmso.itp, line 81]: No default Ryckaert-Bell. types ERROR 8 [file dmso.itp, line 82]: No default Ryckaert-Bell. types ERROR 9 [file dmso.itp, line 83]: No default Ryckaert-Bell. types ERROR 10 [file dmso.itp, line 84]: No default Ryckaert-Bell. types ERROR 11 [file dmso.itp, line 85]: No default Ryckaert-Bell. types ERROR 12 [file dmso.itp, line 86]: No default Ryckaert-Bell. types Excluding 3 bonded neighbours molecule type ‘Protein’ Excluding 3 bonded neighbours molecule type ‘LIG’ NOTE 2 [file topol.top, line 43922]: System has non-zero total charge: -1.000000 Total charge should normally be an integer. See [http://www.gromacs.org/Documentation/Floating\_Point\_Arithmetic](http://www.gromacs.org/Documentation/Floating_Point_Arithmetic) for discussion on how close it should be to an integer. WARNING 1 [file topol.top, line 43922]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge J. Chem. Theory Comput. 10 (2014) pp. 381-393 -------- -------- — Thank You — -------- -------- There were 2 notes There was 1 warning * * * Program: gmx grompp, version 2020.1 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1928) Fatal error: There were 12 errors in input file(s) * * * How can I fix this error? ---
**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 17, 2020, 1:02am UTC](https://gromacs.bioexcel.eu/t/error-at-grommp-for-ions-tpr/671/2 "2020-08-17T01:02:30Z")
Use `coulombtype = cutoff` for generating the input `.tpr` for `genion`. The warning message is actually irrelevant since you’re not actually doing dynamics with this topology. The more pressing issue is the missing dihedrals. You need to provide suitable parameters. ---
**Author:** ![lanselibai](https://avatars.discourse-cdn.com/v4/letter/l/e9c0ed/32.png) [@lanselibai](https://gromacs.bioexcel.eu/u/lanselibai)\ **Post date:** [December 26, 2020, 4:04pm UTC](https://gromacs.bioexcel.eu/t/error-at-grommp-for-ions-tpr/671/3 "2020-12-26T16:04:30Z")
I use the OPLS 2015 version. I have the same problem of `No default Ryckaert-Bell. types` after running `gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1` using Justin’s `ions.mdp` file from his Lysosome tutorial. Use `coulombtype = cutoff` in the `ions.mdp` file still has the same problem. `coulombtype = PME` works fine for the OPLS 2001 version. So is this an issue related to the OPLS 2015 version? How to resolve it? ---
**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:** [December 29, 2020, 2:48am UTC](https://gromacs.bioexcel.eu/t/error-at-grommp-for-ions-tpr/671/4 "2020-12-29T02:48:04Z")
@lanselibai what is in your system? What is(are) the missing dihedral(s)? ---
**Author:** ![lanselibai](https://avatars.discourse-cdn.com/v4/letter/l/e9c0ed/32.png) [@lanselibai](https://gromacs.bioexcel.eu/u/lanselibai)\ **Post date:** [December 29, 2020, 9:20am UTC](https://gromacs.bioexcel.eu/t/error-at-grommp-for-ions-tpr/671/5 "2020-12-29T09:20:01Z")
@jalemkul I have contacted Yale OPLS group. They said they are refining the OPLSAAM. My system is a Fab protein (400 residues). I am not sure how to identify the missing dihedral. Another thing I have found is, 1. when “-inter” is used in the “gmx pdb2gmx”, the “No default Ryckaert-Bell. types” error **still exists** for “gmx grompp -f ions.mdp”. 2. when “-inter” is **not** used in the “gmx pdb2gmx”, the “No default Ryckaert-Bell. types” error **does not exist** for “gmx grompp -f ions.mdp”. ---
**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:** [December 29, 2020, 1:42pm UTC](https://gromacs.bioexcel.eu/t/error-at-grommp-for-ions-tpr/671/6 "2020-12-29T13:42:45Z")
Use of `-inter` doesn’t mean anything unless you made different selections when making the interactive selections. Maybe the difference is in a disulfide or something. But in any case, if a force field is missing dihedrals for common protein terms, it is not complete and therefore not ready for routine use. ---
**Author:** ![lanselibai](https://avatars.discourse-cdn.com/v4/letter/l/e9c0ed/32.png) [@lanselibai](https://gromacs.bioexcel.eu/u/lanselibai)\ **Post date:** [December 29, 2020, 2:14pm UTC](https://gromacs.bioexcel.eu/t/error-at-grommp-for-ions-tpr/671/7 "2020-12-29T14:14:36Z")
Yes, I am not sure why `-inter` causes the differences. But anyway, I will wait for the refinement of `OPLS/AAM` ---
**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:** [January 1, 2021, 1:14am UTC](https://gromacs.bioexcel.eu/t/error-at-grommp-for-ions-tpr/671/8 "2021-01-01T01:14:55Z")
Use `diff` to compare the topologies and you’ll have your answer. ---
**Author:** ![amoltagad115](https://avatars.discourse-cdn.com/v4/letter/a/a183cd/32.png) [@amoltagad115](https://gromacs.bioexcel.eu/u/amoltagad115)\ **Post date:** [February 5, 2021, 2:08pm UTC](https://gromacs.bioexcel.eu/t/error-at-grommp-for-ions-tpr/671/9 "2021-02-05T14:08:15Z")
can you explain how to use diff for identifying missing dihedral s ---
**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 5, 2021, 4:08pm UTC](https://gromacs.bioexcel.eu/t/error-at-grommp-for-ions-tpr/671/10 "2021-02-05T16:08:26Z")
@amoltagad115 in this instance, my advice is to simply generate two topologies and use `diff` to see which lines differ. This will indicate which lines call for interactions that are problematic.