GROMACS version: 2025.0
ERROR 1 [file ERD.itp, line 62]:
No default Bond types for interaction
‘4 13 1’.
ERROR 2 [file ERD.itp, line 176]:
No default U-B types for interaction
‘2 3 4 5’.
ERROR 3 [file ERD.itp, line 183]:
No default U-B types for interaction
‘3 4 13 5’.
ERROR 4 [file ERD.itp, line 185]:
No default U-B types for interaction
‘5 4 13 5’.
ERROR 5 [file ERD.itp, line 187]:
No default U-B types for interaction
‘13 4 24 5’.
ERROR 6 [file ERD.itp, line 208]:
No default U-B types for interaction
‘4 13 14 5’.
ERROR 7 [file ERD.itp, line 232]:
No default Proper Dih. types for interaction
‘1 2 3 4 9’.
ERROR 8 [file ERD.itp, line 241]:
No default Proper Dih. types for interaction
‘4 3 2 15 9’.
ERROR 9 [file ERD.itp, line 242]:
No default Proper Dih. types for interaction
‘2 3 4 5 9’.
ERROR 10 [file ERD.itp, line 243]:
No default Proper Dih. types for interaction
‘2 3 4 13 9’.
ERROR 11 [file ERD.itp, line 244]:
No default Proper Dih. types for interaction
‘2 3 4 24 9’.
ERROR 12 [file ERD.itp, line 249]:
No default Proper Dih. types for interaction
‘13 4 3 22 9’.
ERROR 13 [file ERD.itp, line 250]:
No default Proper Dih. types for interaction
‘13 4 3 23 9’.
ERROR 14 [file ERD.itp, line 253]:
No default Proper Dih. types for interaction
‘3 4 13 14 9’.
ERROR 15 [file ERD.itp, line 254]:
No default Proper Dih. types for interaction
‘5 4 13 14 9’.
ERROR 16 [file ERD.itp, line 255]:
No default Proper Dih. types for interaction
‘6 5 4 13 9’.
ERROR 17 [file ERD.itp, line 257]:
No default Proper Dih. types for interaction
‘12 5 4 13 9’.
ERROR 18 [file ERD.itp, line 287]:
No default Proper Dih. types for interaction
‘14 13 4 24 9’.
ERROR 19 [file ERD.itp, line 288]:
No default Proper Dih. types for interaction
‘4 13 14 15 9’.
ERROR 20 [file ERD.itp, line 289]:
No default Proper Dih. types for interaction
‘4 13 14 16 9’.
ERROR 21 [file ERD.itp, line 296]:
No default Proper Dih. types for interaction
‘2 15 14 13 9’.
ERROR 22 [file ERD.itp, line 299]:
No default Proper Dih. types for interaction
‘2 15 20 21 9’.
Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘ERD’
Excluding 2 bonded neighbours molecule type ‘SOL’
NOTE 2 [file topol.top, line 50336]:
System has non-zero total charge: -12.000000
Total charge should normally be an integer. See
Floating point arithmetic - GROMACS 2025.2 documentation
for discussion on how close it should be to an integer.
atom name 5311 in topol.top and solvated.gro does not match (O1 - C00)
atom name 5311 in topol.top and solvated.gro does not match (O1 - C00)
atom name 5312 in topol.top and solvated.gro does not match (C1 - C01)
atom name 5312 in topol.top and solvated.gro does not match (C1 - C01)
atom name 5313 in topol.top and solvated.gro does not match (C2 - H02)
atom name 5313 in topol.top and solvated.gro does not match (C2 - H02)
atom name 5314 in topol.top and solvated.gro does not match (C3 - O03)
atom name 5314 in topol.top and solvated.gro does not match (C3 - O03)
atom name 5315 in topol.top and solvated.gro does not match (C4 - C04)
atom name 5315 in topol.top and solvated.gro does not match (C4 - C04)
atom name 5316 in topol.top and solvated.gro does not match (C5 - C05)
atom name 5316 in topol.top and solvated.gro does not match (C5 - C05)
atom name 5317 in topol.top and solvated.gro does not match (C6 - C06)
atom name 5317 in topol.top and solvated.gro does not match (C6 - C06)
atom name 5318 in topol.top and solvated.gro does not match (C7 - C07)
atom name 5318 in topol.top and solvated.gro does not match (C7 - C07)
atom name 5319 in topol.top and solvated.gro does not match (O2 - C08)
atom name 5319 in topol.top and solvated.gro does not match (O2 - C08)
atom name 5320 in topol.top and solvated.gro does not match (C8 - C09)
atom name 5320 in topol.top and solvated.gro does not match (C8 - C09)
atom name 5321 in topol.top and solvated.gro does not match (O3 - C0A)
atom name 5321 in topol.top and solvated.gro does not match (O3 - C0A)
atom name 5322 in topol.top and solvated.gro does not match (C9 - O0B)
atom name 5322 in topol.top and solvated.gro does not match (C9 - O0B)
atom name 5323 in topol.top and solvated.gro does not match (O4 - O0C)
atom name 5323 in topol.top and solvated.gro does not match (O4 - O0C)
atom name 5324 in topol.top and solvated.gro does not match (C10 - O0D)
atom name 5324 in topol.top and solvated.gro does not match (C10 - O0D)
atom name 5325 in topol.top and solvated.gro does not match (C11 - C0E)
atom name 5325 in topol.top and solvated.gro does not match (C11 - C0E)
atom name 5326 in topol.top and solvated.gro does not match (C12 - C0F)
atom name 5326 in topol.top and solvated.gro does not match (C12 - C0F)
atom name 5327 in topol.top and solvated.gro does not match (C13 - C0G)
atom name 5327 in topol.top and solvated.gro does not match (C13 - C0G)
atom name 5328 in topol.top and solvated.gro does not match (O5 - C0H)
atom name 5328 in topol.top and solvated.gro does not match (O5 - C0H)
atom name 5329 in topol.top and solvated.gro does not match (C14 - C0I)
atom name 5329 in topol.top and solvated.gro does not match (C14 - C0I)
atom name 5330 in topol.top and solvated.gro does not match (C15 - C0J)
atom name 5330 in topol.top and solvated.gro does not match (C15 - C0J)
(more than 20 non-matching atom names)
(more than 20 non-matching atom names)
WARNING 1 [file topol.top, line 50336]:
33 non-matching atom names
atom names from topol.top will be used
atom names from solvated.gro will be ignored
There were 2 NOTEs
There was 1 WARNING
Program: gmx grompp, version 2025.0
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2400)
Fatal error:
There were 22 errors in input file(s)
For context, my ligand’s .itp has blank columns for b0 and kb in the [bonds] section of the file.