# How to solve no default proper dih. types **URL:** \ **Category:** User discussions\ **Created:** [September 26, 2022, 11:14pm UTC](https://gromacs.bioexcel.eu/t/how-to-solve-no-default-proper-dih-types/4877 "2022-09-26T23:14:18Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![Hanoriega](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hanoriega/32/1562_2.png) [@Hanoriega](https://gromacs.bioexcel.eu/u/Hanoriega)\ **Post date:** [September 26, 2022, 11:14pm UTC](https://gromacs.bioexcel.eu/t/how-to-solve-no-default-proper-dih-types/4877/1 "2022-09-26T23:14:18Z")
GROMACS version: GROMACS modification: Yes/No Here post your question gmx grompp -f em.mdp -p topol.top -c solvate -o em.tpr 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 444956443 Generated 165 of the 1596 non-bonded parameter combinations ERROR 1 [file topol\_Protein\_chain\_A.itp, line 7340]: No default Proper Dih. types ERROR 2 [file topol\_Protein\_chain\_A.itp, line 7341]: No default Proper Dih. types ERROR 3 [file topol\_Protein\_chain\_A.itp, line 7363]: No default Proper Dih. types ERROR 4 [file topol\_Protein\_chain\_A.itp, line 7364]: No default Proper Dih. types ERROR 5 [file topol\_Protein\_chain\_A.itp, line 7390]: No default Proper Dih. types ERROR 6 [file topol\_Protein\_chain\_A.itp, line 7432]: No default Proper Dih. types ERROR 7 [file topol\_Protein\_chain\_A.itp, line 7447]: No default Proper Dih. types ERROR 8 [file topol\_Protein\_chain\_A.itp, line 7448]: No default Proper Dih. types ERROR 9 [file topol\_Protein\_chain\_A.itp, line 7501]: No default Proper Dih. types ERROR 10 [file topol\_Protein\_chain\_A.itp, line 7523]: No default Proper Dih. types ERROR 11 [file topol\_Protein\_chain\_A.itp, line 7619]: No default Proper Dih. types ERROR 12 [file topol\_Protein\_chain\_A.itp, line 7636]: No default Proper Dih. types ERROR 13 [file topol\_Protein\_chain\_A.itp, line 7637]: No default Proper Dih. types ERROR 14 [file topol\_Protein\_chain\_A.itp, line 7660]: No default Proper Dih. types ERROR 15 [file topol\_Protein\_chain\_A.itp, line 7710]: No default Proper Dih. types ERROR 16 [file topol\_Protein\_chain\_A.itp, line 7764]: No default Proper Dih. types ERROR 17 [file topol\_Protein\_chain\_A.itp, line 7815]: No default Proper Dih. types ERROR 18 [file topol\_Protein\_chain\_A.itp, line 7837]: No default Proper Dih. types ERROR 19 [file topol\_Protein\_chain\_A.itp, line 7838]: No default Proper Dih. types ERROR 20 [file topol\_Protein\_chain\_A.itp, line 7964]: No default Proper Dih. types ERROR 21 [file topol\_Protein\_chain\_A.itp, line 7983]: No default Proper Dih. types ERROR 22 [file topol\_Protein\_chain\_A.itp, line 7984]: No default Proper Dih. types ERROR 23 [file topol\_Protein\_chain\_A.itp, line 8067]: No default Proper Dih. types ERROR 24 [file topol\_Protein\_chain\_B.itp, line 23541]: No default Proper Dih. types ERROR 25 [file topol\_Protein\_chain\_B.itp, line 23939]: No default Proper Dih. types ERROR 26 [file topol\_Protein\_chain\_B.itp, line 24185]: No default Proper Dih. types ERROR 27 [file topol\_Protein\_chain\_B.itp, line 24186]: No default Proper Dih. types ERROR 28 [file topol\_Protein\_chain\_B.itp, line 24466]: No default Proper Dih. types ERROR 29 [file topol\_Protein\_chain\_B.itp, line 24818]: No default Proper Dih. types ERROR 30 [file topol\_Protein\_chain\_B.itp, line 24819]: No default Proper Dih. types ERROR 31 [file topol\_Protein\_chain\_B.itp, line 25148]: No default Proper Dih. types ERROR 32 [file topol\_Protein\_chain\_B.itp, line 25421]: No default Proper Dih. types ERROR 33 [file topol\_Protein\_chain\_B.itp, line 25422]: No default Proper Dih. types ERROR 34 [file topol\_Protein\_chain\_B.itp, line 25738]: No default Proper Dih. types ERROR 35 [file topol\_Protein\_chain\_C.itp, line 23541]: No default Proper Dih. types ERROR 36 [file topol\_Protein\_chain\_C.itp, line 23939]: No default Proper Dih. types ERROR 37 [file topol\_Protein\_chain\_C.itp, line 24185]: No default Proper Dih. types ERROR 38 [file topol\_Protein\_chain\_C.itp, line 24186]: No default Proper Dih. types ERROR 39 [file topol\_Protein\_chain\_C.itp, line 24466]: No default Proper Dih. types ERROR 40 [file topol\_Protein\_chain\_C.itp, line 24818]: No default Proper Dih. types ERROR 41 [file topol\_Protein\_chain\_C.itp, line 24819]: No default Proper Dih. types ERROR 42 [file topol\_Protein\_chain\_C.itp, line 25148]: No default Proper Dih. types ERROR 43 [file topol\_Protein\_chain\_C.itp, line 25421]: No default Proper Dih. types ERROR 44 [file topol\_Protein\_chain\_C.itp, line 25422]: No default Proper Dih. types ERROR 45 [file topol\_Protein\_chain\_C.itp, line 25738]: No default Proper Dih. types ERROR 46 [file topol\_Protein\_chain\_E.itp, line 11401]: No default Proper Dih. types ERROR 47 [file topol\_Protein\_chain\_E.itp, line 11402]: No default Proper Dih. types ERROR 48 [file topol\_Protein\_chain\_E.itp, line 11999]: No default Proper Dih. types ERROR 49 [file topol\_Protein\_chain\_E.itp, line 12000]: No default Proper Dih. types ERROR 50 [file topol\_Protein\_chain\_E.itp, line 12331]: No default Proper Dih. types ERROR 51 [file topol\_Protein\_chain\_D.itp, line 11401]: No default Proper Dih. types ERROR 52 [file topol\_Protein\_chain\_D.itp, line 11402]: No default Proper Dih. types ERROR 53 [file topol\_Protein\_chain\_D.itp, line 11999]: No default Proper Dih. types ERROR 54 [file topol\_Protein\_chain\_D.itp, line 12000]: No default Proper Dih. types ERROR 55 [file topol\_Protein\_chain\_D.itp, line 12331]: No default Proper Dih. types Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_A’ Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_B’ Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_C’ Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_E’ Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_D’ Excluding 2 bonded neighbours molecule type ‘SOL’ WARNING 1 [file topol.top, line 54]: The GROMOS force fields have been parametrized with a physically incorrect multiple-time-stepping scheme for a twin-range cut-off. When used with a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), physical properties, such as the density, might differ from the intended values. Since there are researchers actively working on validating GROMOS with modern integrators we have not yet removed the GROMOS force fields, but you should be aware of these issues and check if molecules in your system are affected before proceeding. Further information is available at [https://redmine.gromacs.org/issues/2884](https://redmine.gromacs.org/issues/2884) , and a longer explanation of our decision to remove physically incorrect algorithms can be found at [On The Importance of Accurate Algorithms for Reliable Molecular Dynamics Simulations | Theoretical and Computational Chemistry | ChemRxiv | Cambridge Open Engage](https://doi.org/10.26434/chemrxiv.11474583.v1) . NOTE 2 [file topol.top, line 54]: System has non-zero total charge: 3.000000 Total charge should normally be an integer. See [Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Floating_Point_Arithmetic) for discussion on how close it should be to an integer. WARNING 2 [file topol.top, line 54]: 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 were 2 warnings * * * Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1928) Fatal error: There were 55 errors 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) I tried to do the de-bug at line 730 which I found as a potential, but it did not work it keeps giving me the same error. How do I know what to resolve all these errors? Thanks ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [September 28, 2022, 9:53am UTC](https://gromacs.bioexcel.eu/t/how-to-solve-no-default-proper-dih-types/4877/2 "2022-09-28T09:53:53Z")
Hi, Some extra information may be useful. How did you generate the topology file? Did you use any modified version of the force field? How do these lines look like? > ERROR 1 [file topol\_Protein\_chain\_A.itp, line 7340]: > No default Proper Dih. types > ERROR 2 [file topol\_Protein\_chain\_A.itp, line 7341]: > No default Proper Dih. types \Alessandra ---
**Author:** ![Hanoriega](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hanoriega/32/1562_2.png) [@Hanoriega](https://gromacs.bioexcel.eu/u/Hanoriega)\ **Post date:** [September 28, 2022, 5:02pm UTC](https://gromacs.bioexcel.eu/t/how-to-solve-no-default-proper-dih-types/4877/3 "2022-09-28T17:02:41Z")
Thank you for your response, I created the topol.top through gromacs and forcefield was Charmm. I realized I used -ignh on the first topol.top. I think that is what caused the fail, as it was reading some of the H improperly. I deleted the H through another software and ran again and it created the em.gro file, so it was successful mdrun. On to the next trouble shoot :) Heather ---
**Author:** ![Shivani\_madaan](https://avatars.discourse-cdn.com/v4/letter/s/ecae2f/32.png) [@Shivani\_madaan](https://gromacs.bioexcel.eu/u/Shivani_madaan)\ **Post date:** [June 26, 2023, 7:32am UTC](https://gromacs.bioexcel.eu/t/how-to-solve-no-default-proper-dih-types/4877/4 "2023-06-26T07:32:45Z")
Hello mam Mam I am also getting the same errors which you are getting after running "gmx grompp -f ions.mdp -c prot\_solv.gro -p topol.top -o ions.tpr " this command. Mam may you tell exactly which command you have ran to create topology file. Kindly help me.I appreciate your time and look forward to hearing from you soon.[quote=“Hanoriega, post:3, topic:4877, full:true”] Thank you for your response, I created the topol.top through gromacs and forcefield was Charmm. I realized I used -ignh on the first topol.top. I think that is what caused the fail, as it was reading some of the H improperly. I deleted the H through another software and ran again and it created the em.gro file, so it was successful mdrun. On to the next trouble shoot :) Heather [/quote] Thank you Shivani ---
**Author:** ![Jyothilakshmi](https://avatars.discourse-cdn.com/v4/letter/j/e8c25b/32.png) [@Jyothilakshmi](https://gromacs.bioexcel.eu/u/Jyothilakshmi)\ **Post date:** [August 2, 2023, 11:40am UTC](https://gromacs.bioexcel.eu/t/how-to-solve-no-default-proper-dih-types/4877/5 "2023-08-02T11:40:03Z")
Hey, how did you identify the H atoms which are to be deleted? In my case the error lines being referred to is blank in the last column, was it the same for you ?