GROMACS version:2022.3
GROMACS modification: No
Here post your question:
my peptide sequence is: F-P-ORN-A-W-Y, I want the NE of the sidechain of ORN to form an amide bond with the C-terminus of the peptide.
I add ‘Tyr C 1 Orn NE 1 0.136 Tyr Orn’ into the specbond.dat, after I ran gmx pdb2gmx in Amber99sb-ildn ff, the C-N bond was formed between OC2 and NE. However, additional atoms like OC1 of Tyr and HE1, HE2 and HE3 of Orn are also connected to the C-N bond. I checked the input pdb file there is O of Tyr exist, but no OC1, OC2, HE1, HE2 and HE3 exist.
Could you please let me know what I did wrong and how to form a correct amide bond? Thank you very much.
Cheers,
Wu