[gmx-users] adding hydrogens to protein with pdb2gmx

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Tue Sep 4 17:21:35 CEST 2012

Hi everybody,
when I want the program "pdb2gmx" only to create a topology file but not
to change anything at the protein. Not even adding hydrogen atoms to the
Because my protein already has hydrogen atoms. I only added one residue
and I want to minimize this residue now.

Do I have to call it like this:

pdb2gmx -f inputProtein.pdb -o outputProtein.gro -p protein.top -i
posre.itp  -water none -ff amber03 -ignh

Is that right?

Thank you

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