[gmx-users] using .pdb file from protein data bank

[Madhuri Agashe]

Hi,
I want to use a pdb file from the protein data bank and run a MD simulation
on it.

How does gromacs treat the pdb file taken directly from the protein data
bank? Are protonation sites checked or protonation/deprotonation done?

How can I check the total charge on the protein before starting the
silmulation?