GROMACS version: 2018.6
GROMACS modification: No
I was trying to generate .gro file from a pdb file using pdb2gmx with CHARMM22* force field. The N terminal of my peptide is acetylated Asn and the C terminal is amidated Ala. When I ran the pdb2gmx command with -ignh and -ter, I chose “None” when being prompted to select termini types, and I got the error:
Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your
coordinate file, add a new terminal database entry (.tdb), or select the
proper existing terminal entry.
Is there anything I can do to fix it? Thank you!!