# GROMACS throwing errors on charmm GUI output

**URL:** <https://gromacs.bioexcel.eu/t/gromacs-throwing-errors-on-charmm-gui-output/5003>\
**Category:** User discussions\
**Tags:** forcefield, grompp\
**Created:** [October 12, 2022, 6:13pm UTC](https://gromacs.bioexcel.eu/t/gromacs-throwing-errors-on-charmm-gui-output/5003 "2022-10-12T18:13:59Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![CJWRW](https://avatars.discourse-cdn.com/v4/letter/c/e274bd/32.png) [@CJWRW](https://gromacs.bioexcel.eu/u/CJWRW)\
**Post date:** [October 12, 2022, 6:13pm UTC](https://gromacs.bioexcel.eu/t/gromacs-throwing-errors-on-charmm-gui-output/5003/1 "2022-10-12T18:13:59Z")

</div>

GROMACS version: 2021  
GROMACS modification: Yes/No  
Here post your question  
I have used the charmm GUI to form a bilayer consisting of ceramide 3, CHOL and LIGNP.  
Eventually in my models I will be using gmx insert-molecule to add adjunct molecules with parameters from the CHARMM ligand reader and modeller. Hence I intended to use the full CHARMM36 forcefield. I sourced the latest version from:  
[https://mackerell.umaryland.edu/charmm\_ff.shtml#charmm](https://mackerell.umaryland.edu/charmm_ff.shtml#charmm)  
charmm36-jul2021.ff.tgz

When attempting to gromp the resulting Charmm gui files with the topol.top including the forcefield error I am returned the following errors:  
Command line:  
gmx grompp -f step6.0\_minimization.mdp -c step5\_input.gro -r step5\_input.gro -p topol.top -o min.tpr

Setting the LD random seed to 2147413325

Generated 167799 of the 167910 non-bonded parameter combinations  
Generating 1-4 interactions: fudge = 1

Generated 117519 of the 167910 1-4 parameter combinations

ERROR 1 [file CER3.itp, line 164]:  
No default Bond types

ERROR 2 [file CER3.itp, line 168]:  
No default Bond types

ERROR 3 [file CER3.itp, line 684]:  
No default U-B types

ERROR 4 [file CER3.itp, line 686]:  
No default U-B types

ERROR 5 [file CER3.itp, line 687]:  
No default U-B types

ERROR 6 [file CER3.itp, line 689]:  
No default U-B types

ERROR 7 [file CER3.itp, line 690]:  
No default U-B types

ERROR 8 [file CER3.itp, line 691]:  
No default U-B types

ERROR 9 [file CER3.itp, line 693]:  
No default U-B types

ERROR 10 [file CER3.itp, line 694]:  
No default U-B types

ERROR 11 [file CER3.itp, line 696]:  
No default U-B types

ERROR 12 [file CER3.itp, line 697]:  
No default U-B types

ERROR 13 [file CER3.itp, line 698]:  
No default U-B types

ERROR 14 [file CER3.itp, line 957]:  
No default Proper Dih. types

ERROR 15 [file CER3.itp, line 958]:  
No default Proper Dih. types

ERROR 16 [file CER3.itp, line 959]:  
No default Proper Dih. types

ERROR 17 [file CER3.itp, line 960]:  
No default Proper Dih. types

ERROR 18 [file CER3.itp, line 961]:  
No default Proper Dih. types

ERROR 19 [file CER3.itp, line 962]:  
No default Proper Dih. types

ERROR 20 [file CER3.itp, line 963]:  
No default Proper Dih. types

ERROR 21 [file CER3.itp, line 964]:  
No default Proper Dih. types

ERROR 22 [file CER3.itp, line 965]:  
No default Proper Dih. types

ERROR 23 [file CER3.itp, line 966]:  
No default Proper Dih. types

ERROR 24 [file CER3.itp, line 967]:  
No default Proper Dih. types

ERROR 25 [file CER3.itp, line 969]:  
No default Proper Dih. types

ERROR 26 [file CER3.itp, line 970]:  
No default Proper Dih. types

ERROR 27 [file CER3.itp, line 971]:  
No default Proper Dih. types

ERROR 28 [file CER3.itp, line 972]:  
No default Proper Dih. types

ERROR 29 [file CER3.itp, line 973]:  
No default Proper Dih. types

ERROR 30 [file CER3.itp, line 974]:  
No default Proper Dih. types

ERROR 31 [file CER3.itp, line 975]:  
No default Proper Dih. types

ERROR 32 [file CER3.itp, line 976]:  
No default Proper Dih. types

ERROR 33 [file CER3.itp, line 977]:  
No default Proper Dih. types

ERROR 34 [file CER3.itp, line 978]:  
No default Proper Dih. types

Excluding 3 bonded neighbours molecule type ‘LIGNP’

turning H bonds into constraints…

Excluding 3 bonded neighbours molecule type ‘CHL1’

turning H bonds into constraints…

Excluding 3 bonded neighbours molecule type ‘CER3’

turning H bonds into constraints…

Excluding 2 bonded neighbours molecule type ‘TIP3’

turning H bonds into constraints…

* * *

Program: gmx grompp, version 2021-MODIFIED  
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1963)

Fatal error:  
There were 34 errors in input file(s)