Charges of residues

User discussions
1

GROMACS version:
GROMACS modification: No

Dear all,

I wonder whether the charged residues such as Lys, Arg, Asp, Glu and His residues, as well as the N and C termini are automatically set in charged state when using pdb2gmx command to transfer the pdb file to the gro file format. How could we check the charge state of these residues in a simulation system? How could we change the charge state of these residues? And how could I set the charge state of the system if I wish to simulation at specific pH?

Thank you in advance!

2

pdb2gmx automatically assigns protonation states using canonical pKa values and assuming pH 7. If you want to change protonation states, you can do this with command-line options. See the pdb2gmx help information.