[gmx-users] Protein at given pH

[Steven Neumann]

Dear Gmx Users,

I am trying to simulate protein-ligand interactions at specific pH=5.
I processed my protein.pdb into the H++. As I see from th titration
curve of the entire molecule it appears that at pH=5 the total charge
should be equal to 2. When I process the obtained pdb from the server
to pdb2gmx using -ignh I get the total charge of -3. Can anyone
explain me this?

In terms of small molecules how can I get parameters at specific pH? I
am using Charmm and parachem.org does not support pH changes. Can
anyone advise?

thank you,

Steven