[gmx-users] Simulation of protein at specific pH

prerna bhardwaj prernab2010 at gmail.com
Sun Apr 24 20:43:19 CEST 2011

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

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