# Help with error in topolgy **URL:** \ **Category:** User discussions\ **Created:** [July 2, 2021, 7:47pm UTC](https://gromacs.bioexcel.eu/t/help-with-error-in-topolgy/2445 "2021-07-02T19:47:22Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![rammun23](https://avatars.discourse-cdn.com/v4/letter/r/a4c791/32.png) [@rammun23](https://gromacs.bioexcel.eu/u/rammun23)\ **Post date:** [July 2, 2021, 7:47pm UTC](https://gromacs.bioexcel.eu/t/help-with-error-in-topolgy/2445/1 "2021-07-02T19:47:22Z")
GROMACS version: 2020.4 GROMACS modification: No I tried to run the grompp function with a topology file generated using the pdb2gmx function. I received the following errors, but the lines referenced in the errors do not suggest anything wrong with the topology file. I would appreciate any insights. Errors: ERROR 1 [file topol.top, line 127]: No default Ryckaert-Bell. types ERROR 2 [file topol.top, line 128]: No default Ryckaert-Bell. types ERROR 3 [file topol.top, line 129]: No default Ryckaert-Bell. types ---
**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:** [July 3, 2021, 4:58pm UTC](https://gromacs.bioexcel.eu/t/help-with-error-in-topolgy/2445/2 "2021-07-03T16:58:36Z")
What force field did you use? What sets of atoms are defined on these lines? If you’re getting an error, clearly the parameters are not defined in the force field, but `pdb2gmx` should never write such a topology. Have you modified the force field in any way, or are you dealing with some kind of non-standard species? ---
**Author:** ![rammun23](https://avatars.discourse-cdn.com/v4/letter/r/a4c791/32.png) [@rammun23](https://gromacs.bioexcel.eu/u/rammun23)\ **Post date:** [July 3, 2021, 5:27pm UTC](https://gromacs.bioexcel.eu/t/help-with-error-in-topolgy/2445/3 "2021-07-03T17:27:22Z")
@jalemkul We have a sort of niche application. I am trying to model a small acid-base system in water. I have previously run acetic acid and pyridine using the opslaa support. I am trying to adjust the relative strength of the acid and or base with similar molecules. In this step, I was trying to run a minimization on trifluoroacetic acid in order to generate an itp file for the molecule. I tried the same with 2-methylpyridine and I got the same error in reference to different lines. I did generate a custom rtp file for the system I am working with following a tutorial for methane in water. The following shows the topology file generated using the pdb2gmx function. ; ; File ‘topol.top’ was generated ; By user: Ramson (1006) ; On host: mako ; At date: Fri Jul 2 19:29:47 2021 ; ; This is a standalone topology file ; ; Created by: ; :-) GROMACS - gmx pdb2gmx, 2020.4 (-: ; ; Executable: /usr/local/gromacs/bin/gmx ; Data prefix: /usr/local/gromacs ; Working dir: /home/Ramson/2MP\_Acetic\_Water ; Command line: ; gmx pdb2gmx -f 2\_Met\_Pyr.pdb ; Force field was read from current directory or a relative path - path added. ; ; Include forcefield parameters #include “./oplsaa\_edit.ff/forcefield.itp” [moleculetype] ; Name nrexcl Other 3 [atoms] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 2MP rtp 2MP q 0.0 1 opls\_520 1 2MP N 1 -0.678 14.0067 2 opls\_521 1 2MP C31 1 0.473 12.011 3 opls\_521 1 2MP C32 1 0.473 12.011 4 opls\_523 1 2MP C5 1 0.227 12.011 5 opls\_522 1 2MP C41 1 -0.447 12.011 6 opls\_522 1 2MP C42 1 -0.447 12.011 7 opls\_525 1 2MP H61 1 0.155 1.008 8 opls\_526 1 2MP H7 1 0.065 1.008 9 opls\_525 1 2MP H62 1 0.155 1.008 10 opls\_524 1 2MP H51 1 0.012 1.008 11 opls\_670 1 2MP C6 1 -0.168 12.011 12 opls\_140 1 2MP H8 1 0.06 1.008 13 opls\_140 1 2MP H9 1 0.06 1.008 14 opls\_140 1 2MP H10 1 0.06 1.008 ; qtot 0 [bonds] ; ai aj funct c0 c1 c2 c3 1 2 1 1 3 1 2 5 1 2 10 1 3 6 1 3 11 1 4 5 1 4 6 1 4 8 1 5 7 1 6 9 1 11 12 1 11 13 1 11 14 1 [pairs] ; ai aj funct c0 c1 c2 c3 1 4 1 1 7 1 1 9 1 1 12 1 1 13 1 1 14 1 2 6 1 2 8 1 2 11 1 3 5 1 3 8 1 3 10 1 4 10 1 4 11 1 5 9 1 6 7 1 6 12 1 6 13 1 6 14 1 7 8 1 7 10 1 8 9 1 9 11 1 [angles] ; ai aj ak funct c0 c1 c2 c3 2 1 3 1 1 2 5 1 1 2 10 1 5 2 10 1 1 3 6 1 1 3 11 1 6 3 11 1 5 4 6 1 5 4 8 1 6 4 8 1 2 5 4 1 2 5 7 1 4 5 7 1 3 6 4 1 3 6 9 1 4 6 9 1 3 11 12 1 3 11 13 1 3 11 14 1 12 11 13 1 12 11 14 1 13 11 14 1 [dihedrals] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 3 1 2 5 3 3 1 2 10 3 2 1 3 6 3 2 1 3 11 3 1 2 5 4 3 1 2 5 7 3 10 2 5 4 3 10 2 5 7 3 1 3 6 4 3 1 3 6 9 3 11 3 6 4 3 11 3 6 9 3 1 3 11 12 3 1 3 11 13 3 1 3 11 14 3 6 3 11 12 3 6 3 11 13 3 6 3 11 14 3 6 4 5 2 3 6 4 5 7 3 8 4 5 2 3 8 4 5 7 3 5 4 6 3 3 5 4 6 9 3 8 4 6 3 3 8 4 6 9 3 ; Include Position restraint file #ifdef POSRES #include “posre.itp” #endif [system] ; Name 2-Methyl-Pyridine [molecules] ; Compound #mols Other 1 For reference, I am a beginner to gromacs. I am an undergraduate student working on this project as an independent study so my background knowledge on the subject is not immense. I would appreciate patience if I do not understand right away. Thank you! ---
**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:** [July 3, 2021, 5:39pm UTC](https://gromacs.bioexcel.eu/t/help-with-error-in-topolgy/2445/4 "2021-07-03T17:39:57Z")
The error you’re getting from `grompp` says your molecule has one or more dihedrals that haven’t been parametrized. You need to develop parameters for those missing interactions, or assign them by analogy to similar chemical groups.