GROMACS version:
GROMACS modification: Yes/No
Here post your question
While running the following topology writing command with pdb2gmx for my protein :
gmx pdb2gmx -f 3HTB_clean.pdb -o 3HTB_processed.gro -ter
I received following error can anyone help me resolve it
Fatal error: Atom HB3 in residue SER 6 was not found in rtp entry SER with 13 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 & H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input.
Have you followed this advice?