HIS Protonation Assignment using pdb2gmx

User discussions
1

Dear all,

I want to confirm my understanding of how the protonation state of histidine is assigned in GROMACS (based on the code in hizzie.cpp):
GROMACS estimates virtual hydrogen positions at ND1 and NE2 in HIS, checks if they could act as H-bond donors, and assigns the protonation state accordingly — HSP if both donate, HSD or HSE if only one does, and defaults to HSE if neither does.

Could you please confirm whether this analysis considers the entire structure, including inter-chain hydrogen bonds (e.g., between segid A and B)?

Best regards,
Miriam

2

I checked the code and it only checks intra-moleculetype hydrogen bonds. You could use the -merge option to merge the two chains into one moleculetype to get the automation to work.