No default Bond types

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1

topol.top (1.2 MB)
CAB_fix_str.dat (6.1 KB)

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GROMACS modification: Yes/No
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HI All,

I am facing an error while system preparation at solvation step. I need some help to resolve this. I am attaching the required files here. (I have changed the file extensions just for the sake of upload)

Appreciate your time and response.

Bests
Farhan

Error is as following:

ERROR 1 [file topol.top, line 4886]:
No default Bond types

ERROR 2 [file topol.top, line 4892]:
No default Bond types

ERROR 3 [file topol.top, line 21573]:
No default U-B types

ERROR 4 [file topol.top, line 21576]:
No default U-B types

ERROR 5 [file topol.top, line 21578]:
No default U-B types

ERROR 6 [file topol.top, line 21580]:
No default U-B types

ERROR 7 [file topol.top, line 21581]:
No default U-B types

ERROR 8 [file topol.top, line 21582]:
No default U-B types

ERROR 9 [file topol.top, line 21583]:
No default U-B types

ERROR 10 [file topol.top, line 21588]:
No default U-B types

ERROR 11 [file topol.top, line 21590]:
No default U-B types

ERROR 12 [file topol.top, line 21592]:
No default U-B types

ERROR 13 [file topol.top, line 21593]:
No default U-B types

ERROR 14 [file topol.top, line 21594]:
No default U-B types

ERROR 15 [file topol.top, line 21595]:
No default U-B types

ERROR 16 [file topol.top, line 29944]:
No default Proper Dih. types

ERROR 17 [file topol.top, line 29945]:
No default Proper Dih. types

ERROR 18 [file topol.top, line 29946]:
No default Proper Dih. types

ERROR 19 [file topol.top, line 29947]:
No default Proper Dih. types

ERROR 20 [file topol.top, line 29948]:
No default Proper Dih. types

ERROR 21 [file topol.top, line 29949]:
No default Proper Dih. types

ERROR 22 [file topol.top, line 29950]:
No default Proper Dih. types

ERROR 23 [file topol.top, line 29951]:
No default Proper Dih. types

ERROR 24 [file topol.top, line 29952]:
No default Proper Dih. types

ERROR 25 [file topol.top, line 29953]:
No default Proper Dih. types

ERROR 26 [file topol.top, line 29954]:
No default Proper Dih. types

ERROR 27 [file topol.top, line 29955]:
No default Proper Dih. types

ERROR 28 [file topol.top, line 29977]:
No default Proper Dih. types

ERROR 29 [file topol.top, line 29978]:
No default Proper Dih. types

ERROR 30 [file topol.top, line 29979]:
No default Proper Dih. types

ERROR 31 [file topol.top, line 29980]:
No default Proper Dih. types

ERROR 32 [file topol.top, line 29981]:
No default Proper Dih. types

ERROR 33 [file topol.top, line 29982]:
No default Proper Dih. types

ERROR 34 [file topol.top, line 29983]:
No default Proper Dih. types

ERROR 35 [file topol.top, line 29984]:
No default Proper Dih. types

ERROR 36 [file topol.top, line 29985]:
No default Proper Dih. types

ERROR 37 [file topol.top, line 29990]:
No default Proper Dih. types

ERROR 38 [file topol.top, line 29991]:
No default Proper Dih. types

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’

Excluding 3 bonded neighbours molecule type ‘CAB’

Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 2 [file topol.top, line 43322]:
System has non-zero total charge: -1.819997
Total charge should normally be an integer.

There were 2 notes

Program: gmx grompp, version 2021.3
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1963)

Fatal error:
There were 38 errors in input file(s)

2

cab_prm.dat (1.8 KB)
cab_itp.dat (13.9 KB)

Additional files are attached here

3

Your issue is not related to the ligand. You have chosen an incorrect (chemically impossible) protonation state for the N-terminal proline residue. You cannot use the default “NH3+” terminus type, you need to use “PRO-NH2+” instead. This will fix the fractional charge and the misassigned atom types.

1 Like
4

Hi,

I would like to thank you for your response. It is fixed indeed.

Bests
Farhan