GROMACS version: 2025.0
GROMACS modification: No
Tried to run pdb2gmx on pdb file from OpenMM+grand simulation to prepare topology file, but got an error:
gmx pdb2gmx -f 2ZFF_1A_gcmc_3d_npt.pdb -ter
...
Program: gmx pdb2gmx, version 2025.0
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 896)
Fatal error:
Atom H1 in residue ACE 1 was not found in rtp entry ACE with 6 atoms
while sorting atoms.
For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.
I thought -ter
option will give me choice for protein caps, but not in this case.
How can I solve this issue?
2ZFF_1A_gcmc_3d_npt.txt (3.0 MB)