GROMACS version: 2021
GROMACS modification: Yes/No
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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
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)