# How can I solve the problem: No default Proper Dih. types

**URL:** <https://gromacs.bioexcel.eu/t/how-can-i-solve-the-problem-no-default-proper-dih-types/5427>\
**Category:** User discussions\
**Tags:** grompp\
**Created:** [December 13, 2022, 4:05am UTC](https://gromacs.bioexcel.eu/t/how-can-i-solve-the-problem-no-default-proper-dih-types/5427 "2022-12-13T04:05:01Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![yangying](https://avatars.discourse-cdn.com/v4/letter/y/87869e/32.png) [@yangying](https://gromacs.bioexcel.eu/u/yangying)\
**Post date:** [December 13, 2022, 4:05am UTC](https://gromacs.bioexcel.eu/t/how-can-i-solve-the-problem-no-default-proper-dih-types/5427/1 "2022-12-13T04:05:01Z")

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GROMACS version:gromacs/2021.4-cuda-11.6.0  
GROMACS modification: Yes/No  
Here post your question  
When I was trying to add ions to my system, I used the following command:  
gmx\_mpi grompp -f ions.mdp -c 1ane\_solv.gro -r 1ane\_solv.gro -p topol.top -o ions.tpr -maxwarn 4  
But I get the errors like this:  
ERROR 1 [file topol.top, line 11245]:  
No default Proper Dih. types

ERROR 2 [file topol.top, line 11485]:  
No default Proper Dih. types

ERROR 3 [file topol.top, line 12002]:  
No default Proper Dih. types

ERROR 4 [file topol.top, line 12003]:  
No default Proper Dih. types

ERROR 5 [file topol.top, line 12050]:  
No default Proper Dih. types

ERROR 6 [file topol.top, line 12051]:  
No default Proper Dih. types

ERROR 7 [file topol.top, line 12198]:  
No default Proper Dih. types

ERROR 8 [file topol.top, line 12277]:  
No default Proper Dih. types

ERROR 9 [file topol.top, line 12380]:  
No default Proper Dih. types

ERROR 10 [file topol.top, line 12454]:  
No default Proper Dih. types

ERROR 11 [file topol.top, line 12455]:  
No default Proper Dih. types

ERROR 12 [file topol.top, line 12521]:  
No default Proper Dih. types

ERROR 13 [file topol.top, line 12615]:  
No default Proper Dih. types

ERROR 14 [file topol.top, line 12709]:  
No default Proper Dih. types

I used GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9),

And the following are steps before add ions,  
#Make the position restraint files.  
echo “Make the position restraint files.” \>&2  
${GMXRUN} pdb2gmx -f $1.pdb -o 1\_processed.gro -water spce -posrefc 250 -i posre250.itp \< pdbgmx.txt {GMXRUN} pdb2gmx -f $1.pdb -o 1\_processed.gro -water spce -posrefc 500 -i posre500.itp \< pdbgmx.txt {GMXRUN} pdb2gmx -f $1.pdb -o 1\_processed.gro -water spce -posrefc 750 -i posre750.itp \< pdbgmx.txt {GMXRUN} pdb2gmx -f $1.pdb -o $1\_processed.gro -water spce -posrefc 1000 -i posre1000.itp \< pdbgmx.txt

#Set the water box configuration  
echo “Set the water box configuration” \>&2  
${GMXRUN} editconf -f $1\_processed.gro -o $1\_newbox.gro -c -d 1.0 -bt cubic

#Solvate that box  
echo “Solvate that box” \>&2  
${GMXRUN} solvate -cp $1\_newbox.gro -cs spc216.gro -o $1\_solv.gro -p topol.top

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<div class="post-metadata">

**Author:** ![therealchrisneale](https://avatars.discourse-cdn.com/v4/letter/t/779978/32.png) [@therealchrisneale](https://gromacs.bioexcel.eu/u/therealchrisneale)\
**Post date:** [December 13, 2022, 5:33pm UTC](https://gromacs.bioexcel.eu/t/how-can-i-solve-the-problem-no-default-proper-dih-types/5427/2 "2022-12-13T17:33:17Z")

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`
ERROR 1 [file topol.top, line 11245]:
`

what is on line 11245 of topol.top and what molecule does it refer to and what atoms of that molecule does it refer to?

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<div class="post-metadata">

**Author:** ![yangying](https://avatars.discourse-cdn.com/v4/letter/y/87869e/32.png) [@yangying](https://gromacs.bioexcel.eu/u/yangying)\
**Post date:** [December 14, 2022, 12:42am UTC](https://gromacs.bioexcel.eu/t/how-can-i-solve-the-problem-no-default-proper-dih-types/5427/3 "2022-12-14T00:42:56Z")

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Thank you for your reply. I try to do simulations for a protein, which is from PDB.

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/a/a57883ddcaaee45efa4825fbc052f92c59acb5e0.png)  
so atoms should be 24(O),23(C),25(N),27(C)

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<div class="post-metadata">

**Author:** ![yangying](https://avatars.discourse-cdn.com/v4/letter/y/87869e/32.png) [@yangying](https://gromacs.bioexcel.eu/u/yangying)\
**Post date:** [December 18, 2022, 8:21pm UTC](https://gromacs.bioexcel.eu/t/how-can-i-solve-the-problem-no-default-proper-dih-types/5427/4 "2022-12-18T20:21:34Z")

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I try to do simulations for a protein, and when I run this command  
gmx\_mpi grompp -f ions.mdp -c 1ane\_solv.gro -r 1ane\_solv.gro -p topol.top -o ions.tpr -maxwarn 4  
I got the No default Proper Dih. types error, but I have little experience about this error, I tried to delete the lines in top.tol that are related to this error, it worked, but I am not sure the fix method is right or not?

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**Author:** ![therealchrisneale](https://avatars.discourse-cdn.com/v4/letter/t/779978/32.png) [@therealchrisneale](https://gromacs.bioexcel.eu/u/therealchrisneale)\
**Post date:** [December 23, 2022, 3:01pm UTC](https://gromacs.bioexcel.eu/t/how-can-i-solve-the-problem-no-default-proper-dih-types/5427/5 "2022-12-23T15:01:59Z")

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Not a good idea to simply remove the lines. Suggest figure out where those lines came from and why you are missing the parameters for them. You’d probably get more traffic if you explain how you generated your topology and what your system is. If you did everything correctly, then it’s possible that your issue is related to GMXLIB, moving things in your directory structure so they are no longer where gmx expects them to be, or even an automated scratch filesystem purge on your cluster removing some files. If you made the topology incorrectly, then we don’t have enough information to know what might have been wrong. I did look at what you posted and those look like standard atoms, so I can’t guess why the parameters are not being found.

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**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, 9:38am UTC](https://gromacs.bioexcel.eu/t/how-can-i-solve-the-problem-no-default-proper-dih-types/5427/6 "2023-08-02T09:38:37Z")

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Hey i would like to know how you resolved this, if you have. Thank you