Dear Gromacs User,<br><br>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.<br>
<br>Thanks<br>Prerna<br>