Recently I used HOXB13 protein for MD simulation by Gromacs. When I run OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) I got a fetal error and that Atom HA3 in residue GLY 1 was not found in rtp entry GLY with 9 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.
Please help me and what will be the command if i want to remove H atom from pdb file.
Thanks in advance.