[gmx-users] problem in defining protonation state of amino acids

[Tushar Ranjan Moharana]

Hi everyone,
I want to do a constant pH simulation of my protein using CHARMM36. I
calculated protonation state of various amino acid at required pH using H++
server. However when trying to run pdb2gmx got fatal error "Atom HB3 in
residue SER 3 was not found in rtp entry SER with 11 atoms while sorting
atoms". I can remove the error by adding -ignh but my concerned is this may
change the protonation state. Please help me with your valuable
suggestion.

Thanks for your time and effort.

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB