Atom HD1 in residue HIS was not found in rtp entry HSE with 17 atoms while sorting atoms

User discussions
1

GROMACS version: 2022
GROMACS modification: No

I’m using pdb2gmx to create a topology for my protein. I get an error for HIS residue. I know it’s because of the protonation state, and what I have in my pdb is HSD. I’m just wondering why it doesn’t automatically map HIS with all HSE/HSE/HSP residues, to see which one fits it. How do you deal with this issue?

2

Which forcefield you are using? you can change the protonation state using appropriate flag from gmx pdb2gmx

3

I’m using charmm27. which flag should I use?