Dear Gromacs User, I want to simulate my protein at a specific pH. Using H++ server I have generated my .pdb file at pH 5. But pdb2gmx is showing all the usual fatal error "like "Atom HB3 in residue MET 1 not found in rtp entry with 17 atoms". But I can't use -ignh option, because it is bringing back at the same normal stage. So what should I do I want to carry out simulation at pH 5.
Thanks Prerna
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