How to solve no default proper dih. types

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1

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 , 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 .

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
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

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

2

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

3

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

4

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

5

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 ?